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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/augur">Debian Med / augur</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/27276569a04fc5522af19ef3d73f0393a754b8ed">27276569</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-09T21:36:33+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/cdaaf80484e2308591a59e27565d2abaaa365539">cdaaf804</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-09T21:36:34+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.0.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/2a334376333cbcc971fd7615080fcd90526dfa49">2a334376</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-09T21:37:48+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/10.0.4'
Update to upstream version '10.0.4'
with Debian dir 6195cab8fb73e919524e4676797389fec9ed4a75</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/b59a1a7a9dcc7b11889c92a0c2605a20f37262b7">b59a1a7a</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-09T21:38:01+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
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</li>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">
augur/__version__.py
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<li class="file-stats">
<a href="#1058ed03848375e3c1a8b82623654cb578984455">
augur/filter.py
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<li class="file-stats">
<a href="#5aa84eddf9e5286c15160859a367e2b67129d7d8">
augur/tree.py
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#2001bad2a6274a7936c111e6f05a1fa33ebc08f7">
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+
devel/test
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/augur/-/compare/76c71d0ebbf0065f663f8e5c24af7becbbf5a395...b59a1a7a9dcc7b11889c92a0c2605a20f37262b7#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,16 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## __NEXT__</span></span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 10.0.4 (6 November 2020)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> tree: Use a more generic approach to escape special characters from alignment sequence names prior to running IQ-TREE <span class="p">[</span><span class="nv" style="color: #008080;">#625</span><span class="p">][]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> filter: Reduce memory usage by not reading sequences into memory <span class="p">[</span><span class="nv" style="color: #008080;">#627</span><span class="p">][]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#625</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/625</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#627</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/627</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 10.0.3 (23 October 2020)</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<li id="a1a05fb3eb681edc11e8c987f65967f416af0ee1">
<a href="https://salsa.debian.org/med-team/augur/-/compare/76c71d0ebbf0065f663f8e5c24af7becbbf5a395...b59a1a7a9dcc7b11889c92a0c2605a20f37262b7#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'10.0.<span class="idiff left right">3</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC1" 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;">'10.0.<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_augur_version_compatible</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/76c71d0ebbf0065f663f8e5c24af7becbbf5a395...b59a1a7a9dcc7b11889c92a0c2605a20f37262b7#1058ed03848375e3c1a8b82623654cb578984455"><strong>augur/filter.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">@@ -139,7 +139,7 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if Fasta, read in file to get sequence names and sequences</span></span>
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<pre style="margin: 0;"> <span id="LC140" 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="LC141" 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="LC142" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">to_dict</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqIO</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">parse</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sequences</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'fasta'</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">index</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sequences</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'fasta'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: Problem reading in {}:"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">error</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">@@ -394,11 +394,24 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">write_vcf</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">dropped_samps</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">seq_to_keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">seq</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">,</span><span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_keep</span><span class="p">]</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="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;">seq_to_keep</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="LC397" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># It is possible to have ids in the list of sequences to keep that do</span></span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># not exist in the original input sequences. Find the intersection of</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># these two lists of ids to determine if all samples were dropped or</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># not. This final list of ids is in the same order as the input</span></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sequences such that output sequences are always in the same order for</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># a given set of filters.</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">seq_to_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">seq_id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqs</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_keep</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="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;">seq_to_write</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="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: All samples have been dropped! Check filter rules and metadata file format."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">seq_to_keep</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write out sequences that passed all filters using an iterator to</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ensure that sequences are streamed to disk without being read into</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># memory first.</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">seq_to_keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">seq_id</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_to_write</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">sequences_written</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">seq_to_keep</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%i sequences were dropped during filtering"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">all_seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq_keep</span><span class="p">),))</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">exclude</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/76c71d0ebbf0065f663f8e5c24af7becbbf5a395...b59a1a7a9dcc7b11889c92a0c2605a20f37262b7#5aa84eddf9e5286c15160859a367e2b67129d7d8"><strong>augur/tree.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">@@ -133,18 +133,29 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> aln_file file name of input aligment</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> out_file file name to write tree to</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">aln_file</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ifile</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">tmp_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ifile</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># create a dictionary for characters that IQ-tree changes.</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we remove those prior to tree-building and reinstantiate later</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;">random_string</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">string</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ascii_uppercase</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">letters</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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;">letters</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">letters</span><span class="p">),</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DELIM"</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">escape_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">c</span><span class="p">:</span><span class="s" style="color: #d14;">f'_</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">prefix</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">random_string</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">)</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">_'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">'/|()*'</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">reverse_escape_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">k</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">escape_dict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()}</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># IQ-tree messes with taxon names. Hence remove offending characters, reinstaniate later</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">tmp_aln_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln_file</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">".fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-delim.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_aln_file</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">".fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">".iqtree.log"</span><span class="p">)</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">num_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ofile</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">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;">tmp_seqs</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ofile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">aln_file</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ifile</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" 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;">ifile</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">tmp_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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145
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="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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146
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">num_seqs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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147
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<td class="diff-line-num new_line old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">ofile</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">,</span> <span class="s" style="color: #d14;">'_X_X_'</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="p">,</span><span class="s" style="color: #d14;">'_Y_Y_'</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"("</span><span class="p">,</span><span class="s" style="color: #d14;">"_X_Y_"</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">")"</span><span class="p">,</span><span class="s" style="color: #d14;">"_Y_X_"</span><span class="p">))</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">escape_dict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">tmp_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_line</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">ofile</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">tmp_line</span><span class="p">)</span></span>
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148
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>
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149
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For compat with older versions of iqtree, we avoid the newish -fast</span></span>
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150
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># option alias and instead spell out its component parts:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,7 +206,10 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt</td>
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195
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Phylo</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".treefile"</span><span class="p">,</span> <span class="s" style="color: #d14;">'newick'</span><span class="p">)</span></span>
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196
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".treefile"</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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197
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">T</span><span class="p">.</span><span class="n" style="color: #333;">find_clades</span><span class="p">(</span><span class="n" style="color: #333;">terminal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_X_X_'</span><span class="p">,</span><span class="s" style="color: #d14;">'/'</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_Y_Y_'</span><span class="p">,</span><span class="s" style="color: #d14;">'|'</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"_X_Y_"</span><span class="p">,</span><span class="s" style="color: #d14;">"("</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"_Y_X_"</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="LC209" class="line" lang="python"> <span class="n" style="color: #333;">tmp_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span><span class="p">,</span><span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reverse_escape_dict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">tmp_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_name</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_name</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#this allows the user to check intermediate output, as tree.nwk will be</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clean_up</span><span class="p">:</span></span>
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#allow user to see chosen model if modeltest was run</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/76c71d0ebbf0065f663f8e5c24af7becbbf5a395...b59a1a7a9dcc7b11889c92a0c2605a20f37262b7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">augur (10.0.4-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Mon, 09 Nov 2020 21:38:01 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">augur (10.0.3-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Augur is installable only for Architecture: amd64 i386 due to its</span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/76c71d0ebbf0065f663f8e5c24af7becbbf5a395...b59a1a7a9dcc7b11889c92a0c2605a20f37262b7#2001bad2a6274a7936c111e6f05a1fa33ebc08f7"><strong>devel/test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Runs tests in a sandboxed environment that loosely replicates the Travis CI</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># environment.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-euo</span> pipefail</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Conda functions are not exported into a new bash environment by default, so we</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># need to source the conda profile script from the current conda installation.</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This script expects PS1 to be defined, so we set it to an empty value.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PS1</span><span class="o" style="font-weight: 600;">=</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">conda_dir</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>conda info <span class="nt" style="color: #000080;">--base</span><span class="si" style="color: #d14;">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">conda_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/etc/profile.d/conda.sh"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Install Augur from the current directory into a new conda environment.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">conda <span class="nb" style="color: #0086b3;">env </span>create <span class="nt" style="color: #000080;">-f</span> environment.yml</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">conda activate augur</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pip <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-e</span> .[dev]</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run unit and functional tests.</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">./run_tests.sh</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">bash tests/builds/runner.sh</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Clean up the temporary environment.</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">conda deactivate</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">conda <span class="nb" style="color: #0086b3;">env </span>remove <span class="nt" style="color: #000080;">-n</span> augur</span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/76c71d0ebbf0065f663f8e5c24af7becbbf5a395...b59a1a7a9dcc7b11889c92a0c2605a20f37262b7#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,7 +71,7 @@ setuptools.setup(</td>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">"pytest-cov >=2.8.1, ==2.8.*"</span><span class="p">,</span></span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">"pytest-mock >= 2.0.0, ==2.0.*"</span><span class="p">,</span></span>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"recommonmark >=0.5.0, ==0.*"</span><span class="p">,</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">"snakemake >=5.4.0, <span class="idiff left right">==5.*</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">"snakemake >=5.4.0, <span class="idiff left right"><5.27</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">"Sphinx >=2.0.1, ==2.*"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"sphinx-argparse >=0.2.5, ==0.*"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"sphinx-markdown-tables >= 0.0.9"</span><span class="p">,</span></span>
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