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<h3>
Liubov Chuprikova pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/q2-demux">Debian Med / q2-demux</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb">ff693221</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2019-12-29T15:11:37Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2019.10.0</pre>
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<h4>24 changed files:</h4>
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q2_demux/__init__.py
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q2_demux/_filter.py
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q2_demux/_summarize/_visualizer.py
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q2_demux/_version.py
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q2_demux/plugin_setup.py
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q2_demux/tests/test_demux.py
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setup.py
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<h4>Changes:</h4>
<li id="107803585d618ad2e75911856735aa3b99cf9b48">
<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#107803585d618ad2e75911856735aa3b99cf9b48"><strong>q2_demux/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(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="9" style="width: 35px; color: rgba(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">@@ -9,6 +9,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(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="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._demux</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">emp_single</span><span class="p">,</span> <span class="n" style="color: #333;">emp_paired</span></span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(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="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._subsample</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">subsample_single</span><span class="p">,</span> <span class="n" style="color: #333;">subsample_paired</span></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(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="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._summarize</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">summarize</span></span>
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<td class="diff-line-num new old_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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<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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">filter_samples</span></span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(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="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_versions</span></span>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,4 +17,4 @@ __version__ = get_versions()['version']</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">get_versions</span></span>
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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="python"></span>
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(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="LC19" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'emp_single'</span><span class="p">,</span> <span class="s" style="color: #d14;">'emp_paired'</span><span class="p">,</span> <span class="s" style="color: #d14;">'summarize'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'subsample_single'</span><span class="p">,</span> <span class="s" style="color: #d14;">'subsample_paired'</span><span class="p">]</span></span></pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'subsample_single'</span><span class="p">,</span> <span class="s" style="color: #d14;">'subsample_paired'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'filter_samples'</span></span><span class="p">]</span></span></pre>
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<li id="3162594f2e3fedde92c8821b49a2aacc136bb3e6">
<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#3162594f2e3fedde92c8821b49a2aacc136bb3e6"><strong>q2_demux/_filter.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metadata</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">duplicate</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_types.per_sample_sequences</span> <span class="kn" style="font-weight: 600;">import</span> \</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">CasavaOneEightSingleLanePerSampleDirFmt</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._summarize</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_PlotQualView</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_samples</span><span class="p">(</span><span class="n" style="color: #333;">demux</span><span class="p">:</span> <span class="n" style="color: #333;">_PlotQualView</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">:</span> <span class="n" style="color: #333;">Metadata</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">exclude_ids</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</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="LC23" class="line" lang="python"> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">CasavaOneEightSingleLanePerSampleDirFmt</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CasavaOneEightSingleLanePerSampleDirFmt</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">demux</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">demux</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">directory_format</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">ids_to_keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ids</span><span class="p">(</span><span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">where</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">ids_to_keep</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'No filtering requested.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">manifest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">manifest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</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;">if</span> <span class="n" style="color: #333;">exclude_ids</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">ids_to_keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">manifest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">ids_to_keep</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ids_to_keep</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">forward</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">manifest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">forward</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">duplicate</span><span class="p">(</span><span class="n" style="color: #333;">forward</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">forward</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">manifest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reverse</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">duplicate</span><span class="p">(</span><span class="n" style="color: #333;">reverse</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">reverse</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'{id!r} is not a sample present in the '</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">'demultiplexed data.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">results</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#9fdc148f8aba30f25155a319b1195b51d3195d8f"><strong>q2_demux/_summarize/_visualizer.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">@@ -25,7 +25,7 @@ TEMPLATES = pkg_resources.resource_filename('q2_demux', '_summarize')</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_decode_qual_to_phred33</span><span class="p">(</span><span class="n" style="color: #333;">qual_str</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this function is adapted from scikit-bio</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from<span class="idiff left">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">qual_str</span></span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uint8</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">33</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from<span class="idiff left">buffer</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">qual_str</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">encode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'ascii'</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uint8</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">33</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">qual</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#d6bb17df1f3a430ff0853f91968d4b4bdb5b402a"><strong>q2_demux/_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">@@ -23,9 +23,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 2019.<span class="idiff left right">4.1</span>)"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">7d08f111ea34d99d7eb77a3583eaf839ecfde05b</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-<span class="idiff left right">05-08 16:42:34 -07</span>00"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 2019.<span class="idiff left right">10.0</span>)"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">aec76a7d22d7126b57b99da259d752e72e99f148</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-<span class="idiff left right">11-01 01:04:23 +00</span>00"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#c56f147e7d5f7ae43ff9af300d7a45a6a7f28d62"><strong>q2_demux/plugin_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">@@ -9,8 +9,10 @@</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">importlib</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.plugin</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">Plugin</span><span class="p">,</span> <span class="n" style="color: #333;">MetadataColumn</span><span class="p">,</span> <span class="n" style="color: #333;">Categorical</span><span class="p">,</span> <span class="n" style="color: #333;">Bool</span><span class="p">,</span> <span class="n" style="color: #333;">Int</span><span class="p">,</span> <span class="n" style="color: #333;">Float</span><span class="p">,</span> <span class="n" style="color: #333;">Range</span><span class="p">,</span> <span class="n" style="color: #333;">Citations</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">Plugin</span><span class="p">,</span> <span class="n" style="color: #333;">Metadata</span><span class="p">,</span> <span class="n" style="color: #333;">MetadataColumn</span><span class="p">,</span> <span class="n" style="color: #333;">Categorical</span><span class="p">,</span> <span class="n" style="color: #333;">Bool</span><span class="p">,</span> <span class="n" style="color: #333;">Str</span><span class="p">,</span> <span class="n" style="color: #333;">Int</span><span class="p">,</span> <span class="n" style="color: #333;">Float</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">Range</span><span class="p">,</span> <span class="n" style="color: #333;">Citations</span><span class="p">,</span> <span class="n" style="color: #333;">TypeMatch</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_types.sample_data</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SampleData</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_types.per_sample_sequences</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">SequencesWithQuality</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndSequencesWithQuality</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">@@ -228,4 +230,43 @@ plugin.methods.register_function(</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="s" style="color: #d14;">'sequences after subsampling.'</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>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC233" 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;">TypeMatch</span><span class="p">([</span><span class="n" style="color: #333;">SequencesWithQuality</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndSequencesWithQuality</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">JoinedSequencesWithQuality</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">methods</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_function</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">q2_demux</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter_samples</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'demux'</span><span class="p">:</span> <span class="n" style="color: #333;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">T</span><span class="p">]},</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'metadata'</span><span class="p">:</span> <span class="n" style="color: #333;">Metadata</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="s" style="color: #d14;">'where'</span><span class="p">:</span> <span class="n" style="color: #333;">Str</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="s" style="color: #d14;">'exclude_ids'</span><span class="p">:</span> <span class="n" style="color: #333;">Bool</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'filtered_demux'</span><span class="p">,</span> <span class="n" style="color: #333;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">T</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">input_descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="s" style="color: #d14;">'demux'</span><span class="p">:</span> <span class="s" style="color: #d14;">'The demultiplexed data from which samples should be '</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="s" style="color: #d14;">'filtered.'</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">parameter_descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="s" style="color: #d14;">'metadata'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Sample metadata indicating which sample ids to filter. '</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="s" style="color: #d14;">'The optional `where` parameter may be used to filter ids '</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">'based on specified conditions in the metadata. The '</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="s" style="color: #d14;">'optional `exclude_ids` parameter may be used to exclude '</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="s" style="color: #d14;">'the ids specified in the metadata from the filter.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="s" style="color: #d14;">'where'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Optional SQLite WHERE clause specifying sample metadata '</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="s" style="color: #d14;">'criteria that must be met to be included in the filtered '</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="s" style="color: #d14;">'data. If not provided, all samples in `metadata` that are '</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="s" style="color: #d14;">'also in the demultiplexed data will be retained.'</span><span class="p">,</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="s" style="color: #d14;">'exclude_ids'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Defaults to False. If True, the samples selected by '</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="s" style="color: #d14;">'the `metadata` and optional `where` parameter will be '</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="s" style="color: #d14;">'excluded from the filtered data.'</span><span class="p">,</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="p">},</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">output_descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="s" style="color: #d14;">'filtered_demux'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Filtered demultiplexed data.'</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Filter samples out of demultiplexed data.'</span><span class="p">,</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Filter samples indicated in given metadata out of '</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;">'demultiplexed data. Specific samples can be further selected '</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="s" style="color: #d14;">'with the WHERE clause, and the `exclude_ids` parameter '</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="s" style="color: #d14;">'allows for filtering of all samples not specified.'</span><span class="p">,</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"><span class="p">)</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"></span>
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231
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"><span class="n" style="color: #333;">importlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'q2_demux._transformer'</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#a1724a92c10e2b4086443336e3a387d544e2cad5"><strong>q2_demux/tests/data/filter_samples_paired_end/dir_fmt/MANIFEST</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sample-id,filename,direction</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sample1,sample1_1_L001_R1_001.fastq.gz,forward</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">sample1,sample1_1_L001_R2_001.fastq.gz,reverse</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">sample2,sample2_2_L001_R1_001.fastq.gz,forward</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">sample2,sample2_2_L001_R2_001.fastq.gz,reverse</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#6f4303c587cf6c42767602f8b863a7e8b9098502"><strong>q2_demux/tests/data/filter_samples_paired_end/dir_fmt/metadata.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">phred-offset</span><span class="pi">:</span> <span class="m" style="color: #099;">33</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#SampleID Study</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sample1 A</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">sample2 B</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#SampleID Study</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">1 A</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#SampleID Study</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sample1 A</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#c6376f7abe23203a89da8ffaf5010892c7707403"><strong>q2_demux/tests/data/filter_samples_single_end/dir_fmt/MANIFEST</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sample-id,filename,direction</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># direction is not meaningful in this file as these</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># data may be derived from forward, reverse, or</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># joined reads</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">sample1,sample1_1_L001_R1_001.fastq.gz,forward</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">sample2,sample2_2_L001_R1_001.fastq.gz,forward</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">phred-offset</span><span class="pi">:</span> <span class="m" style="color: #099;">33</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#SampleID Study</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sample1 A</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">sample2 B</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#SampleID Study</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">1 A</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#323c5a8b0299834513c6826acf1938385af18615"><strong>q2_demux/tests/data/filter_samples_single_end/filter_subset.tsv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#SampleID Study</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sample1 A</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#da35b2fe9fd2766fcd66820fe8fa96375009cf7b"><strong>q2_demux/tests/test_demux.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">@@ -18,7 +18,6 @@ import pandas as pd</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pdt</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">skbio</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">npt</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.plugin.testing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestPluginBase</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">@@ -28,7 +27,8 @@ from q2_demux import emp_single, emp_paired, summarize</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_types.per_sample_sequences</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">FastqGzFormat</span><span class="p">,</span> <span class="n" style="color: #333;">FastqManifestFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_demux._summarize._visualizer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_PlotQualView</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_demux._summarize._visualizer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">_PlotQualView</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">_decode_qual_to_phred33</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BarcodeSequenceFastqIteratorTests</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -172,17 +172,12 @@ class BarcodeSequenceFastqIteratorTests(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">EmpTestingUtils</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_decode_qual_to_phred</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">qual_str</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this function is adapted from scikit-bio</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fromstring</span><span class="p">(</span><span class="n" style="color: #333;">qual_str</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uint8</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">33</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">qual</span></span>
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<pre style="margin: 0;">-<span id="LC179" 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;">_compare_sequence_to_record</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">fields</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;">header_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'description'</span><span class="p">]])</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:],</span> <span class="n" style="color: #333;">header_line</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_decode_qual_to_phred</span></span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_decode_qual_to_phred33</span></span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">positional_metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'quality'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_compare_manifests</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">act_manifest</span><span class="p">,</span> <span class="n" style="color: #333;">exp_manifest</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2019, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metadata</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.plugin.testing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestPluginBase</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_types.per_sample_sequences</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">SingleLanePerSamplePairedEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_demux._filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">filter_samples</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_demux._summarize</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_PlotQualView</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FilterSamplesTests</span><span class="p">(</span><span class="n" style="color: #333;">TestPluginBase</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">package</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'q2_demux.tests'</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setUp</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">data_single</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_single_end/dir_fmt'</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;">'r'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_PlotQualView</span><span class="p">(</span><span class="n" style="color: #333;">data_single</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="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">manifest_single</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data_single</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">manifest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_single_end/filter_all.tsv'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_subset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_single_end/filter_subset.tsv'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_none</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_single_end/filter_none.tsv'</span><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;">data_paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleLanePerSamplePairedEndFastqDirFmt</span><span class="p">(</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_paired_end/dir_fmt'</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;">'r'</span><span class="p">)</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_PlotQualView</span><span class="p">(</span><span class="n" style="color: #333;">data_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">manifest_paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data_paired</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">manifest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_single_end/filter_all.tsv'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_subset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_single_end/filter_subset.tsv'</span><span class="p">))</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_none</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'filter_samples_single_end/filter_none.tsv'</span><span class="p">))</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_assert_single_contains</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp_ids</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">obs_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">))]</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">obs_ids</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">exp_ids</span><span class="p">))</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_assert_paired_contains</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp_ids</span><span class="p">):</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">obs_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">))]</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">obs_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="nb" style="color: #0086b3;">id</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="nb" style="color: #0086b3;">id</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">obs_ids</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">obs_ids</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">exp_ids</span><span class="p">))</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2'</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">]),</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2'</span><span class="p">]),</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2'</span><span class="p">])]</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_all</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="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_single_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_all_exclude</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="LC76" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[]),</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2'</span><span class="p">]),</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">]),</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[])]</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_all</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_single_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</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>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_subset</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">]),</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">])]</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_subset</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_single_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_subset_no_filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</span><span class="p">]</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</span><span class="p">:</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</span><span class="p">):</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_subset</span><span class="p">,</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_subset_exclude</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2'</span><span class="p">]),</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2'</span><span class="p">]),</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2'</span><span class="p">])]</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_subset</span><span class="p">,</span> <span class="n" style="color: #333;">where</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="LC108" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_single_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_sinlge_subset_exclude_no_filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</span><span class="p">]</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</span><span class="p">:</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</span><span class="p">):</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_subset</span><span class="p">,</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_none_exclude</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2'</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="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2'</span><span class="p">]),</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2'</span><span class="p">])]</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_none</span><span class="p">,</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_single_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"></span>
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_id_not_present</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">]</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</span><span class="p">:</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">):</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_none</span><span class="p">,</span> <span class="n" style="color: #333;">where</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;">False</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>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_none_no_filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</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;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</span><span class="p">:</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_none</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_single_none_exclude_no_filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</span><span class="p">]</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</span><span class="p">:</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</span><span class="p">):</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_single</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_single_none</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">'sample2R2'</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="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">]),</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</span><span class="p">]),</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">,</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</span><span class="p">])]</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_all</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;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_paired_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</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>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_all_exclude</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="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="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</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="p">(</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">]),</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[])]</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_all</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;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">True</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_paired_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_subset</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</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 class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">]),</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</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;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_subset</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_paired_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</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>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_subset_no_filtering</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</span><span class="p">]</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</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;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</span><span class="p">):</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_subset</span><span class="p">,</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_subset_exclude</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</span><span class="p">]),</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</span><span class="p">]),</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</span><span class="p">])]</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_subset</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_paired_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_subset_exclude_no_filtering</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</span><span class="p">]</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</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="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</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;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_subset</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="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_none_exclude</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">exps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</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="p">(</span><span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R1'</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="s" style="color: #d14;">'sample2R2'</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="p">(</span><span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample1R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample1R2'</span><span class="p">,</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">'sample2R1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample2R2'</span><span class="p">])]</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">exps</span><span class="p">:</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">dir_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_none</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_assert_paired_contains</span><span class="p">(</span><span class="n" style="color: #333;">dir_fmt</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_id_not_present</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' OR Study='B'"</span><span class="p">]</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</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="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">):</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_none</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_paired_none_no_filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</span><span class="p">]</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</span><span class="p">:</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</span><span class="p">):</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_none</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"></span>
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226
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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;">test_filter_paired_none_exclude_no_filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="n" style="color: #333;">wheres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Study='B'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Study='A' AND Study='B'"</span><span class="p">]</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wheres</span><span class="p">:</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'No'</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;">filter_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample_paired</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">md_paired_none</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-demux/commit/ff6932213e5dc598ad500abce0b1884e8e575cdb#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">@@ -33,6 +33,10 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'data/single_sample_multiple_files/*'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'data/subsample_single_end/*'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'data/subsample_paired_end/*'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">'data/filter_samples_single_end/*'</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;">'data/filter_samples_single_end/dir_fmt/*'</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;">'data/filter_samples_paired_end/*'</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;">'data/filter_samples_paired_end/dir_fmt/*'</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 class="s" style="color: #d14;">'q2_demux'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'_summarize/assets/*.html'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'_summarize/assets/dist/*'</span><span class="p">,</span></span>
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