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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/augur">Debian Med / augur</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913">f4634e10</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-01-16T08:12:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.1.0</pre>
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<h4>20 changed files:</h4>
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.travis.yml
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">
augur/__version__.py
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<a href="#73daf62265fd7608625d8a35b16297aed2a2399e">
augur/ancestral.py
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<a href="#75dd11b179bed0c75a7e63134345d60a147c6525">
augur/data/lat_longs.tsv
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<a href="#3ed70fb067595a65b1e4bf8038592dae0fd7e371">
augur/data/schema-auspice-config-v2.json
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<a href="#02d8e8d598b529460bef6fc54111c5e51a47fe25">
augur/data/schema-export-v1-meta.json
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<a href="#14b5faf9162fd5951ca5a90c2809eb597852d4c3">
augur/data/schema-export-v1-tree.json
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augur/data/schema-export-v2.json
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augur/filter.py
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<a href="#5aa84eddf9e5286c15160859a367e2b67129d7d8">
augur/tree.py
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docs/contribute/DEV_DOCS.md
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tests/builds/zika.t
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tests/functional/filter.t
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tests/functional/tree.t
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tests/functional/tree/aligned.fasta.xz
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tests/functional/tree/excluded_sites.txt
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tests/test_align.py
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tests/test_filter_groupby.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s" style="color: #d14;">~> </span><span class="m" style="color: #099;">1.0</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">generic</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># See <https://docs.travis-ci.com/user/build-stages/> for more information on</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># how build stages work.</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">stages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">test</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># See <https://docs.travis-ci.com/user/conditions-v1> for more on the "if" syntax.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">branch = release and type != pull_request</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="nl">&test</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">test</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.6</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash miniconda.sh -b -p $HOME/miniconda</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$HOME/miniconda/bin:$PATH"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">hash -r</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda config --set always_yes yes --set changeps1 no</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda update -q conda</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda info -a</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda create -n augur -c bioconda python=$TRAVIS_PYTHON_VERSION mafft raxml fasttree iqtree vcftools pip numpy</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">source activate augur</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install biopython==1.67</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -e .[dev]</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">(pytest -c pytest.python3.ini --cov-report= --cov=augur)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">(cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">(bash tests/builds/runner.sh)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># upload to codecov</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash <(curl -s https://codecov.io/bash) -f "!*.gcov" -X gcov -e TRAVIS_PYTHON_VERSION -y ci/codecov.yml|| echo "Codecov did not collect coverage reports"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*test</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.7</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*test</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">./devel/travis-rebuild-docker-image</span></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,47 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## __NEXT__</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.1.0 (10 December 2021)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Features</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> schemas: Add "$id" key to Auspice config schemas so we have a way of referring to these. <span class="p">[</span><span class="nv" style="color: #008080;">#806</span><span class="p">][]</span> (@tsibley)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">*</span> filter: Fix groupby with incomplete dates. <span class="p">[</span><span class="nv" style="color: #008080;">#808</span><span class="p">][]</span> (@victorlin)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#806</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/806</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#808</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/808</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.0.4 (8 December 2021)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">*</span> dependencies: Replace deprecated mutable sequence interface for BioPython. <span class="p">[</span><span class="nv" style="color: #008080;">#788</span><span class="p">][]</span> (@Carlosbogo)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p">*</span> dependencies: Fix backward compatibility with BioPython. <span class="p">[</span><span class="nv" style="color: #008080;">#801</span><span class="p">][]</span> (@huddlej)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">*</span> data: Add latitude and longitude details for "Reunion". <span class="p">[</span><span class="nv" style="color: #008080;">#791</span><span class="p">][]</span> (@corneliusroemer)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">*</span> filter: Use pandas functions to determine subsample groups. <span class="p">[</span><span class="nv" style="color: #008080;">#794</span><span class="p">][]</span> and <span class="p">[</span><span class="nv" style="color: #008080;">#797</span><span class="p">][]</span> (@victorlin)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">*</span> filter: Add clarity to help message and output of probabilistic sampling. <span class="p">[</span><span class="nv" style="color: #008080;">#792</span><span class="p">][]</span> (@victorlin)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#788</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/788</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#791</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/791</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#792</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/792</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#794</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/794</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#797</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/797</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#801</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/801</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.0.3 (19 November 2021)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="p">*</span> tree: Handle compressed alignment when excluding sites. <span class="p">[</span><span class="nv" style="color: #008080;">#786</span><span class="p">][]</span> (@huddlej)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">*</span> docs: Fix typos (<span class="p">[</span><span class="nv" style="color: #008080;">ce0834c</span><span class="p">][]</span>) and clarify exclude sites inputs (<span class="p">[</span><span class="nv" style="color: #008080;">5ad1574</span><span class="p">][]</span>). (@corneliusroemer)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#786</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/786</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">ce0834c</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/commit/ce0834c476abc9ee99785fa930608218b7d78990</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">5ad1574</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/commit/5ad157485015623883c6b637d247459f906b63cb</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.0.2 (12 October 2021)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.com/nextstrain/augur.svg?branch=master</span><span class="p">)</span>](https://travis-ci.com/nextstrain/augur)</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![PyPI version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://badge.fury.io/py/nextstrain-augur.svg</span><span class="p">)</span>](https://pypi.org/project/nextstrain-augur/)</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/augur/README.html)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Documentation Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest</span><span class="p">)</span>](https://nextstrain<span class="idiff left right">-augur.readthedocs.io/en/stable/?badge=latest</span>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Documentation Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest</span><span class="p">)</span>](https://<span class="idiff left">docs.</span>nextstrain<span class="idiff right">.org/projects/augur/en/stable/</span>)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License: AGPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-AGPL%20v3-blue.svg</span><span class="p">)</span>](https://www.gnu.org/licenses/agpl-3.0)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![DOI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://joss.theoj.org/papers/10.21105/joss.02906/status.svg</span><span class="p">)</span>](https://doi.org/10.21105/joss.02906)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,14 +24,14 @@ The output of augur is a series of JSONs that can be used to visualize your resu</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quickstart</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Follow instructions to install Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain<span class="idiff left right">-augur.readthedocs.io</span>/en/stable/installation/installation.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Follow instructions to install Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">https://<span class="idiff left">docs.</span>nextstrain<span class="idiff right">.org/projects/augur</span>/en/stable/installation/installation.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">Try out an analysis of real virus data by <span class="p">[</span><span class="nv" style="color: #008080;">completing the Zika tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/docs/tutorials/zika</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Documentation</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Overview of how Augur fits together with other Nextstrain tools</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/docs/getting-started/introduction#open-source-tools-for-the-community</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Overview of Augur usage</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/docs/bioinformatics/introduction-to-augur</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Technical documentation for Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain<span class="idiff left right">-augur.readthedocs.io</span>/en/stable/installation/installation.html</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Technical documentation for Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">https://<span class="idiff left">docs.</span>nextstrain<span class="idiff right">.org/projects/augur</span>/en/stable/installation/installation.html</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Contributor guide</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Project board with available issues</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/orgs/nextstrain/projects/6</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Developer docs for Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/contribute/DEV_DOCS.md</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'13.<span class="idiff left right">0.2</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'13.<span class="idiff left right">1.0</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_augur_version_compatible</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#73daf62265fd7608625d8a35b16297aed2a2399e"><strong>augur/ancestral.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,7 +168,7 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">alignment</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Enfore treetime 0.7 or later</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Enfor<span class="idiff left right">c</span>e treetime 0.7 or later</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StrictVersion</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">treetime</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">StrictVersion</span><span class="p">(</span><span class="n" style="color: #333;">treetime</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">StrictVersion</span><span class="p">(</span><span class="s" style="color: #d14;">'0.7.0'</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#75dd11b179bed0c75a7e63134345d60a147c6525"><strong>augur/data/lat_longs.tsv</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">@@ -187,6 +187,7 @@ country portugal 39.6945 -8.13057</td>
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187
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="plaintext">country puerto_rico 18.2459121 -66.4164147</span>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext">country puerto rico 18.2459121 -66.4164147</span>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext">country qatar 25.27932 51.52245</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">country reunion -21.1151 55.5364</span>
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190
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext">country romania 46.0 25.0</span>
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191
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext">country russia 64.6863136 97.7453061</span>
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192
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="plaintext">country rwanda -2.0 30.0</span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#3ed70fb067595a65b1e4bf8038592dae0fd7e371"><strong>augur/data/schema-auspice-config-v2.json</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"v2"</span><span class="p">,</span></span>
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4
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$schema"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"http://json-schema.org/draft-06/schema#"</span><span class="p">,</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$id"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://nextstrain.org/schemas/auspice/config/v2"</span><span class="p">,</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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5
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Auspice config file to be supplied to `augur export v2`"</span><span class="p">,</span></span>
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6
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$comment"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"This schema includes deprecated-but-handled-by-augur-export-v1 properties, but their schema definitions are somewhat incomplete"</span><span class="p">,</span></span>
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7
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"additionalProperties"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">false</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#02d8e8d598b529460bef6fc54111c5e51a47fe25"><strong>augur/data/schema-export-v1-meta.json</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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3
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$schema"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"http://json-schema.org/draft-06/schema#"</span><span class="p">,</span></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0.1"</span><span class="p">,</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$id"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://nextstrain.org/schemas/dataset/v1/meta"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Nextstrain minimal metadata JSON schema"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"This is the validation schema for the augur produced metadata JSON, for consumption in Auspice. Note that every field is optional, but excluding fields may disable certain features in Auspice."</span><span class="p">,</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"additionalProperties"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">true</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#14b5faf9162fd5951ca5a90c2809eb597852d4c3"><strong>augur/data/schema-export-v1-tree.json</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$schema"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"http://json-schema.org/draft-06/schema#"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$id"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://nextstrain.org/schemas/dataset/v1/tree"</span><span class="p">,</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Nextstrain tree JSON schema"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"additionalProperties"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">false</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"required"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"attr"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"strain"</span><span class="p">],</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#fec638407816347df368936c41e5929f42fd4fe6"><strong>augur/data/schema-export-v2.json</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$schema"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"http://json-schema.org/draft-06/schema#"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"$id"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://nextstrain.org/schemas/dataset/v2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"object"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"title"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Nextstrain metadata JSON schema proposal (meta + tree together)"</span><span class="p">,</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"additionalProperties"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">false</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"required"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"version"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"meta"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"tree"</span><span class="p">],</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#1058ed03848375e3c1a8b82623654cb578984455"><strong>augur/filter.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -884,91 +884,76 @@ def get_groups_for_subsampling(strains, metadata, group_by=None):</td>
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"><span class="s" style="color: #d14;"> [{'strain': 'strain1', 'filter': 'skip_group_by_with_ambiguous_month', 'kwargs': ''}]</span></span>
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group_by</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_by</span></span>
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"_dummy"</span><span class="p">,)</span></span>
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">strains</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="python"> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">strains</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="python"> <span class="n" style="color: #333;">skip_strain</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">strain</span><span class="p">].</span><span class="n" style="color: #333;">to_dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># collect group specifiers</span></span>
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groups</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"_dummy"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'date'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC905" 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="LC906" class="line" lang="python"> <span class="n" style="color: #333;">year</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">[</span><span class="s" style="color: #d14;">"date"</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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907
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span></span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC894" 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;">group_by</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">group_by</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</span><span class="p">,):</span></span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">strain</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</span><span class="p">,)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">strains</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span></span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="python"> <span class="n" style="color: #333;">group_by_set</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;">group_by</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If we could not find any requested categories, we cannot complete subsampling.</span></span>
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'date'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">metadata</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">group_by_set</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">{</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">}:</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FilterException</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"The specified group-by categories (</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">group_by</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">) were not found. No sequences-per-group sampling will be done. Note that using 'year' or 'year month' requires a column called 'date'."</span><span class="p">)</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">group_by_set</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">{</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">}):</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FilterException</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"The specified group-by categories (</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">group_by</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">) were not found. No sequences-per-group sampling will be done."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># date requested</span></span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'year'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by_set</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'month'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by_set</span><span class="p">:</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'date'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">metadata</span><span class="p">:</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># set year/month/day = unknown</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"WARNING: A 'date' column could not be found to group-by year or month."</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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"Filtering by group may behave differently than expected!"</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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="python"> <span class="n" style="color: #333;">df_dates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">({</span><span class="s" style="color: #d14;">'year'</span><span class="p">:</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">:</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">([</span><span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">df_dates</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># replace date with year/month/day as nullable ints</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="python"> <span class="n" style="color: #333;">date_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'day'</span><span class="p">]</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">df_dates</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;">'date'</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">expand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="python"> <span class="n" style="color: #333;">df_dates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df_dates</span><span class="p">.</span><span class="n" style="color: #333;">set_axis</span><span class="p">(</span><span class="n" style="color: #333;">date_cols</span><span class="p">[:</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df_dates</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)],</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="919" 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">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="python"> <span class="n" style="color: #333;">missing_date_cols</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;">date_cols</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;">df_dates</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_date_cols</span><span class="p">:</span></span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="python"> <span class="n" style="color: #333;">df_dates</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">NA</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">date_cols</span><span class="p">:</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="python"> <span class="n" style="color: #333;">df_dates</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">to_numeric</span><span class="p">(</span><span class="n" style="color: #333;">df_dates</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">],</span> <span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'coerce'</span><span class="p">).</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Int64Dtype</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">([</span><span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">(</span><span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">df_dates</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'year'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by_set</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># skip ambiguous years</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="python"> <span class="n" style="color: #333;">df_skip</span> <span class="o" style="font-weight: 600;">=</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 class="s" style="color: #d14;">'year'</span><span class="p">].</span><span class="n" style="color: #333;">isnull</span><span class="p">()]</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">subset</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">],</span> <span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df_skip</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">:</span></span>
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908
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="python"> <span class="n" style="color: #333;">skipped_strains</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span></span>
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909
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="python"> <span class="s" style="color: #d14;">"strain"</span><span class="p">:</span> <span class="n" style="color: #333;">strain</span><span class="p">,</span></span>
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910
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="python"> <span class="s" style="color: #d14;">"filter"</span><span class="p">:</span> <span class="s" style="color: #d14;">"skip_group_by_with_ambiguous_year"</span><span class="p">,</span></span>
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="python"> <span class="s" style="color: #d14;">"kwargs"</span><span class="p">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="python"> <span class="p">})</span></span>
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913
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="python"> <span class="n" style="color: #333;">skip_strain</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC914" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'month'</span><span class="p">:</span></span>
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916
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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917
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">month</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">[</span><span class="s" style="color: #d14;">"date"</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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918
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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919
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<pre style="margin: 0;">-<span id="LC919" class="line" lang="python"> <span class="n" style="color: #333;">skipped_strains</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span></span>
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="python"> <span class="s" style="color: #d14;">"strain"</span><span class="p">:</span> <span class="n" style="color: #333;">strain</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="python"> <span class="s" style="color: #d14;">"filter"</span><span class="p">:</span> <span class="s" style="color: #d14;">"skip_group_by_with_ambiguous_month"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="python"> <span class="s" style="color: #d14;">"kwargs"</span><span class="p">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="python"> <span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="python"> <span class="n" style="color: #333;">skip_strain</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC925" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">year</span><span class="p">,</span> <span class="n" style="color: #333;">month</span><span class="p">))</span></span>
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928
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC929" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">year</span><span class="p">)</span></span>
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930
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'unknown'</span><span class="p">)</span></span>
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932
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="python"></span>
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933
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<pre style="margin: 0;">-<span id="LC933" 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;">skip_strain</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">[</span><span class="n" style="color: #333;">strain</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">group</span><span class="p">)</span></span>
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935
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If we could not find any requested categories, we cannot complete subsampling.</span></span>
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937
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="python"> <span class="n" style="color: #333;">distinct_groups</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;">group_by_strain</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>
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938
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<pre style="margin: 0;">-<span id="LC938" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">distinct_groups</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">'unknown'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">distinct_groups</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="s" style="color: #d14;">'unknown'</span><span class="p">,)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">distinct_groups</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="python"> <span class="n" style="color: #333;">error_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"The specified group-by categories (</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">groups</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">) were not found. No sequences-per-group sampling will be done."</span></span>
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<pre style="margin: 0;">-<span id="LC940" class="line" lang="python"></span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groups</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC942" class="line" lang="python"> <span class="n" style="color: #333;">error_message</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" Note that using 'year' or 'year month' requires a column called 'date'."</span></span>
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943
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Raise an exception, since we cannot find the requested groups.</span></span>
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FilterException</span><span class="p">(</span><span class="n" style="color: #333;">error_message</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check to see if some categories are missing to warn the user</span></span>
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="python"> <span class="n" style="color: #333;">group_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="python"> <span class="s" style="color: #d14;">'date'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cat</span></span>
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groups</span></span>
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="python"> <span class="n" style="color: #333;">missing_cats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">cat</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">.</span><span class="n" style="color: #333;">values</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"_dummy"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing_cats</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="python"> <span class="n" style="color: #333;">error_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'date'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_cats</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="python"> <span class="n" style="color: #333;">error_message</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>
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958
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="python"> <span class="s" style="color: #d14;">"Some of the specified group-by categories couldn't be found: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cat</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_cats</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'date'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC959" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'date'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_cats</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="python"> <span class="n" style="color: #333;">error_message</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"A 'date' column could not be found to group-by year or month."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC963" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC964" class="line" lang="python"> <span class="n" style="color: #333;">error_message</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Filtering by group may behave differently than expected!"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print a warning message, but allow grouping to continue.</span></span>
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<pre style="margin: 0;">-<span id="LC967" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC968" class="line" lang="python"> <span class="s" style="color: #d14;">"WARNING: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">error_message</span><span class="p">),</span></span>
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969
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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970
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="python"> <span class="p">)</span></span>
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971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="python"></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'month'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by_set</span><span class="p">:</span></span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># skip ambiguous months</span></span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="python"> <span class="n" style="color: #333;">df_skip</span> <span class="o" style="font-weight: 600;">=</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 class="s" style="color: #d14;">'month'</span><span class="p">].</span><span class="n" style="color: #333;">isnull</span><span class="p">()]</span></span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">subset</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">],</span> <span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df_skip</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">:</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="python"> <span class="n" style="color: #333;">skipped_strains</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="python"> <span class="s" style="color: #d14;">"strain"</span><span class="p">:</span> <span class="n" style="color: #333;">strain</span><span class="p">,</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="python"> <span class="s" style="color: #d14;">"filter"</span><span class="p">:</span> <span class="s" style="color: #d14;">"skip_group_by_with_ambiguous_month"</span><span class="p">,</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="python"> <span class="s" style="color: #d14;">"kwargs"</span><span class="p">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="python"> <span class="p">})</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># month = (year, month)</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">],</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">]))</span></span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: support group by day</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="python"></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="python"> <span class="n" style="color: #333;">unknown_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_by_set</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;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">unknown_groups</span><span class="p">:</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"WARNING: Some of the specified group-by categories couldn't be found: </span><span class="si" style="color: #d14;">{</span><span class="s" style="color: #d14;">', '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">unknown_groups</span><span class="p">)</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Filtering by group may behave differently than expected!"</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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unknown_groups</span><span class="p">:</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'unknown'</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="python"></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="n" style="color: #333;">group_by</span><span class="p">].</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)))</span></span>
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972
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span></span>
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973
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="python"></span>
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1143" style="width: 35px; color: rgba(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="1128" style="width: 35px; color: rgba(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">@@ -1143,7 +1128,7 @@ def register_arguments(parser):</td>
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1143
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="python"> <span class="n" style="color: #333;">subsample_limits_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sequences-per-group'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"subsample to no more than this number of sequences per category"</span><span class="p">)</span></span>
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1144
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1129
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="python"> <span class="n" style="color: #333;">subsample_limits_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--subsample-max-sequences'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"subsample to no more than this number of sequences; can be used without the group_by argument"</span><span class="p">)</span></span>
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1145
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1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="python"> <span class="n" style="color: #333;">probabilistic_sampling_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subsample_group</span><span class="p">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">()</span></span>
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1146
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<pre style="margin: 0;">-<span id="LC1146" class="line" lang="python"> <span class="n" style="color: #333;">probabilistic_sampling_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--probabilistic-sampling'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">Enable</span> probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when `--subsample-max-sequences` is provided."</span><span class="p">)</span></span>
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1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="python"> <span class="n" style="color: #333;">probabilistic_sampling_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--probabilistic-sampling'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">Allow</span> probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when `--subsample-max-sequences` is provided."</span><span class="p">)</span></span>
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1147
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="python"> <span class="n" style="color: #333;">probabilistic_sampling_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--no-probabilistic-sampling'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_false'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'probabilistic_sampling'</span><span class="p">)</span></span>
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1148
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="python"> <span class="n" style="color: #333;">subsample_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--priority'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"""tab-delimited file with list of priority scores for strains (e.g., "<strain></span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t<priority>") and no header.</span></span>
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1149
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="python"><span class="s" style="color: #d14;"> When scores are provided, Augur converts scores to floating point values, sorts strains within each subsampling group from highest to lowest priority, and selects the top N strains per group where N is the calculated or requested number of strains per group.</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">@@ -1494,16 +1479,20 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sequences requested, sequences per group will be a floating point</span></span>
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1480
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<pre style="margin: 0;"> <span id="LC1480" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># value and subsampling will be probabilistic.</span></span>
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1496
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1481
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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1497
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<pre style="margin: 0;">-<span id="LC1497" class="line" lang="python"> <span class="n" style="color: #333;">sequences_per_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculate_sequences_per_group</span><span class="p">(</span></span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="python"> <span class="n" style="color: #333;">sequences_per_group</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">probabilistic_used</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculate_sequences_per_group</span><span class="p">(</span></span>
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1498
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1483
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<pre style="margin: 0;"> <span id="LC1483" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsample_max_sequences</span><span class="p">,</span></span>
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1499
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1484
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="python"> <span class="n" style="color: #333;">records_per_group</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span></span>
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1500
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1485
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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">probabilistic_sampling</span><span class="p">,</span></span>
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1501
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1486
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="python"> <span class="p">)</span></span>
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1502
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<pre style="margin: 0;">-<span id="LC1502" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"Sampling at </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sequences_per_group</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> per group."</span><span class="p">)</span></span>
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1503
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1487
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<pre style="margin: 0;"> <span id="LC1487" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">TooManyGroupsError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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1504
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1488
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<pre style="margin: 0;"> <span id="LC1488" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"ERROR: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">error</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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1505
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1489
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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1506
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1490
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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="python"></span>
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1491
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<pre style="margin: 0;">+<span id="LC1491" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">probabilistic_used</span><span class="p">):</span></span>
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1492
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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"Sampling probabilistically at </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sequences_per_group</span><span class="p">:</span><span class="mf" style="color: #099;">0.4</span><span class="n" style="color: #333;">f</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> sequences per group, meaning it is possible to have more than the requested maximum of </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsample_max_sequences</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> sequences after filtering."</span><span class="p">)</span></span>
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1493
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<pre style="margin: 0;">+<span id="LC1493" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1494
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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"Sampling at </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sequences_per_group</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> per group."</span><span class="p">)</span></span>
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1495
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="python"></span>
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1507
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1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">queues_by_group</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1508
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1497
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<pre style="margin: 0;"> <span id="LC1497" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># We know all of the possible groups now from the first pass through</span></span>
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1498
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<pre style="margin: 0;"> <span id="LC1498" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the metadata, so we can create queues for all groups at once.</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">@@ -1711,7 +1700,7 @@ def numeric_date(date):</td>
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1711
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1700
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<pre style="margin: 0;"> <span id="LC1700" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">treetime</span><span class="p">.</span><span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">numeric_date</span><span class="p">(</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))))</span></span>
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1701
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<pre style="margin: 0;"> <span id="LC1701" class="line" lang="python"></span>
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1713
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1702
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<pre style="margin: 0;"> <span id="LC1702" class="line" lang="python"></span>
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1714
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<pre style="margin: 0;">-<span id="LC1714" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calculate_sequences_per_group</span><span class="p">(</span><span class="n" style="color: #333;">target_max_value</span><span class="p">,</span> <span class="n" style="color: #333;">counts_per_group</span><span class="p">,</span> <span class="n" style="color: #333;">probabilistic</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calculate_sequences_per_group</span><span class="p">(</span><span class="n" style="color: #333;">target_max_value</span><span class="p">,</span> <span class="n" style="color: #333;">counts_per_group</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">allow_</span>probabilistic</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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1715
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1704
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<pre style="margin: 0;"> <span id="LC1704" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate the number of sequences per group for a given maximum number of</span></span>
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1716
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1705
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<pre style="margin: 0;"> <span id="LC1705" class="line" lang="python"><span class="s" style="color: #d14;"> sequences to be returned and the number of sequences in each requested</span></span>
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1717
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1706
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<pre style="margin: 0;"> <span id="LC1706" class="line" lang="python"><span class="s" style="color: #d14;"> group. Optionally, allow the result to be probabilistic such that the mean</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1714" style="width: 35px; color: rgba(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">@@ -1725,7 +1714,7 @@ def calculate_sequences_per_group(target_max_value, counts_per_group, probabilis</td>
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1725
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1714
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<pre style="margin: 0;"> <span id="LC1714" class="line" lang="python"><span class="s" style="color: #d14;"> number of sequences per group for the given counts per group.</span></span>
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1726
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1715
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<pre style="margin: 0;"> <span id="LC1715" class="line" lang="python"><span class="s" style="color: #d14;"> counts_per_group : list[int]</span></span>
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1727
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1716
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<pre style="margin: 0;"> <span id="LC1716" class="line" lang="python"><span class="s" style="color: #d14;"> A list with the number of sequences in each requested group.</span></span>
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1728
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<pre style="margin: 0;">-<span id="LC1728" class="line" lang="python"><span class="s" style="color: #d14;"> probabilistic : bool</span></span>
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1717
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<pre style="margin: 0;">+<span id="LC1717" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">allow_</span>probabilistic : bool</span></span>
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1729
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1718
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<pre style="margin: 0;"> <span id="LC1718" class="line" lang="python"><span class="s" style="color: #d14;"> Whether to allow probabilistic subsampling when the number of groups</span></span>
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1730
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1719
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="python"><span class="s" style="color: #d14;"> exceeds the requested maximum.</span></span>
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1731
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1720
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<pre style="margin: 0;"> <span id="LC1720" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1722" style="width: 35px; color: rgba(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">@@ -1733,29 +1722,35 @@ def calculate_sequences_per_group(target_max_value, counts_per_group, probabilis</td>
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1733
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1722
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<pre style="margin: 0;"> <span id="LC1722" class="line" lang="python"><span class="s" style="color: #d14;"> ------</span></span>
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1734
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1723
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<pre style="margin: 0;"> <span id="LC1723" class="line" lang="python"><span class="s" style="color: #d14;"> TooManyGroupsError :</span></span>
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1735
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1724
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<pre style="margin: 0;"> <span id="LC1724" class="line" lang="python"><span class="s" style="color: #d14;"> When there are more groups than sequences per group and probabilistic</span></span>
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<pre style="margin: 0;">-<span id="LC1736" class="line" lang="python"><span class="s" style="color: #d14;"> subsampling is not <span class="idiff left right">enabl</span>ed.</span></span>
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="python"><span class="s" style="color: #d14;"> subsampling is not <span class="idiff left right">allow</span>ed.</span></span>
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1726
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<pre style="margin: 0;"> <span id="LC1726" class="line" lang="python"></span>
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1727
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<pre style="margin: 0;"> <span id="LC1727" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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1728
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<pre style="margin: 0;"> <span id="LC1728" class="line" lang="python"><span class="s" style="color: #d14;"> -------</span></span>
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1729
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="python"><span class="s" style="color: #d14;"> int or float :</span></span>
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1730
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<pre style="margin: 0;"> <span id="LC1730" class="line" lang="python"><span class="s" style="color: #d14;"> Number of sequences per group.</span></span>
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1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="python"><span class="s" style="color: #d14;"> bool :</span></span>
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="python"><span class="s" style="color: #d14;"> Whether probabilistic subsampling was used.</span></span>
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1733
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<pre style="margin: 0;"> <span id="LC1733" class="line" lang="python"></span>
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1734
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<pre style="margin: 0;"> <span id="LC1734" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC1735" class="line" lang="python"> <span class="n" style="color: #333;">probabilistic_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC1736" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1737" 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="LC1738" class="line" lang="python"> <span class="n" style="color: #333;">sequences_per_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_calculate_sequences_per_group</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1739" class="line" lang="python"> <span class="n" style="color: #333;">target_max_value</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1740" class="line" lang="python"> <span class="n" style="color: #333;">counts_per_group</span><span class="p">,</span></span>
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1741
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<pre style="margin: 0;"> <span id="LC1741" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1742" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">TooManyGroupsError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1750" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">probabilistic</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">allow_probabilistic</span><span class="p">:</span></span>
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1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"WARNING: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">error</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1745" class="line" lang="python"> <span class="n" style="color: #333;">sequences_per_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_calculate_fractional_sequences_per_group</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1746" class="line" lang="python"> <span class="n" style="color: #333;">target_max_value</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1747" class="line" lang="python"> <span class="n" style="color: #333;">counts_per_group</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="python"> <span class="n" style="color: #333;">probabilistic_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC1750" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1751" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">error</span></span>
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<pre style="margin: 0;"> <span id="LC1752" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1758" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sequences_per_group</span></span>
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sequences_per_group</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">probabilistic_used</span></span></span>
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<pre style="margin: 0;"> <span id="LC1754" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1755" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TooManyGroupsError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#5aa84eddf9e5286c15160859a367e2b67129d7d8"><strong>augur/tree.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,11 +8,13 @@ import sys</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uuid</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;">Bio</span></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;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MutableSeq</span></span>
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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;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Phylo</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">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="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime.vcf_utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_vcf</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;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_sequences</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">run_shell_command</span><span class="p">,</span> <span class="n" style="color: #333;">nthreads_value</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">,</span> <span class="n" style="color: #333;">load_mask_sites</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_executable</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -315,7 +317,7 @@ def mask_sites_in_multiple_sequence_alignment(alignment_file, excluded_sites_fil</td>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Load alignment as FASTA generator to prevent loading the whole alignment</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># into memory.</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">Bio</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">SeqIO</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">parse</span></span><span class="p">(</span><span class="n" style="color: #333;">alignment_file</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"fasta"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">read_sequences</span></span><span class="p">(</span><span class="n" style="color: #333;">alignment_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write the masked alignment to disk one record at a time.</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">alignment_file_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">alignment_file</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">@@ -323,7 +325,7 @@ def mask_sites_in_multiple_sequence_alignment(alignment_file, excluded_sites_fil</td>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">masked_alignment_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">oh</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Convert to a mutable sequence to enable masking with Ns.</span></span>
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<pre style="margin: 0;">-<span id="LC326" 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;"><span class="idiff left">record</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tomutable</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC328" 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;"><span class="idiff left">MutableSeq</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Replace all excluded sites with Ns.</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">site</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">excluded_sites</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">@@ -345,7 +347,7 @@ def register_arguments(parser):</td>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--nthreads'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nthreads_value</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of threads to use; specifying the value 'auto' will cause the number of available CPU cores on your system, if determinable, to be used"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--vcf-reference'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'fasta file of the sequence the VCF was mapped to'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--exclude-sites'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'file name of one-based sites to exclude for raw tree building (BED format in .bed files, <span class="idiff left right">DRM format</span> in tab-delimited files, or one position per line)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--exclude-sites'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'file name of one-based sites to exclude for raw tree building (BED format in .bed files, <span class="idiff left right">second column</span> in tab-delimited files, or one position per line)'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--tree-builder-args'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'extra arguments to be passed directly to the executable of the requested tree method (e.g., --tree-builder-args="-czb")'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#73cc809ba2916206462a7eb6005867f214a34fcc"><strong>docs/contribute/DEV_DOCS.md</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">@@ -230,7 +230,7 @@ It can sometimes be useful to verify the config is parsed as you expect using</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contributing documentation</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain<span class="idiff left right">-augur.readthedocs.io</span></span><span class="p">)</span> is built using <span class="p">[</span><span class="nv" style="color: #008080;">Sphinx</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sphinx-doc.org/</span><span class="p">)</span> and hosted on <span class="p">[</span><span class="nv" style="color: #008080;">Read The Docs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://<span class="idiff left">docs.</span>nextstrain<span class="idiff right">.org/projects/augur</span></span><span class="p">)</span> is built using <span class="p">[</span><span class="nv" style="color: #008080;">Sphinx</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sphinx-doc.org/</span><span class="p">)</span> and hosted on <span class="p">[</span><span class="nv" style="color: #008080;">Read The Docs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown">Versions of the documentation for each augur release and git branch are available and preserved.</span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="markdown">Read The Docs is updated automatically from commits and releases on GitHub.</span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#6788c84297b185802f92db51db36c33eb731ecfe"><strong>tests/builds/zika.t</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -54,7 +54,7 @@ Align filtered sequences to a specific reference sequence and fill any gaps.</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="perl"><span class="s1" style="color: #d14;"> > --output "$TMP/out/aligned.fasta" \</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="perl"><span class="s1" style="color: #d14;"> > --fill-gaps > /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="perl"><span class="s1" style="color: #d14;"> $ diff -u "results/aligned.fasta" "$TMP/out/aligned.fasta"</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"><span class="s1" style="color: #d14;"> $ diff <span class="idiff left right">--ignore-matching-lines=".*KX369547.1.*" </span>-u "results/aligned.fasta" "$TMP/out/aligned.fasta"</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="perl"><span class="s1" style="color: #d14;">Build a tree from the multiple sequence alignment.</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#0698fd06e0fd6334ba03f49c4d5fcab894112ff2"><strong>tests/functional/filter.t</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,6 +119,39 @@ By setting the subsample seed above, we should get the same results for both run</td>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ diff -u <(sort "$TMP/filtered_strains_probabilistic.txt") <(sort "$TMP/filtered_strains_default.txt")</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ rm -f "$TMP/filtered_strains_probabilistic.txt" "$TMP/filtered_strains_default.txt"</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="sr" style="color: #009926;">Check output of probabilistic sampling.</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ ${AUGUR} filter \</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --metadata filter/metadata.tsv \</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --group-by region year month \</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-max-sequences 3 \</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --probabilistic-sampling \</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-seed 314159 \</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --output-metadata "$TMP/filtered_metadata.tsv"</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="perl"><span class="sr" style="color: #009926;"> WARNING: Asked to provide at most 3 sequences, but there are 8 groups.</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="perl"><span class="sr" style="color: #009926;"> Sampling probabilistically at 0.3633 sequences per group, meaning it is possible to have more than the requested maximum of 3 sequences after filtering.</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="perl"><span class="sr" style="color: #009926;"> 10 strains were dropped during filtering</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="perl"><span class="sr" style="color: #009926;"> \t1 were dropped during grouping due to ambiguous year information (esc)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="perl"><span class="sr" style="color: #009926;"> \t1 were dropped during grouping due to ambiguous month information (esc)</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="perl"><span class="sr" style="color: #009926;"> \t8 of these were dropped because of subsampling criteria, using seed 314159 (esc)</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="perl"><span class="sr" style="color: #009926;"> 2 strains passed all filters</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="perl"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="perl"><span class="sr" style="color: #009926;">Ensure probabilistic sampling is not used when unnecessary.</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="perl"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ ${AUGUR} filter \</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --metadata filter/metadata.tsv \</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --group-by region year month \</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-max-sequences 10 \</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --probabilistic-sampling \</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-seed 314159 \</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --output-metadata "$TMP/filtered_metadata.tsv"</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl"><span class="sr" style="color: #009926;"> Sampling at 10 per group.</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl"><span class="sr" style="color: #009926;"> 2 strains were dropped during filtering</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl"><span class="sr" style="color: #009926;"> \t1 were dropped during grouping due to ambiguous year information (esc)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl"><span class="sr" style="color: #009926;"> \t1 were dropped during grouping due to ambiguous month information (esc)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl"><span class="sr" style="color: #009926;"> \t0 of these were dropped because of subsampling criteria, using seed 314159 (esc)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="perl"><span class="sr" style="color: #009926;"> 10 strains passed all filters</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="perl"></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl"><span class="sr" style="color: #009926;">Filter using only metadata without sequence input or output and save results as filtered metadata.</span></span>
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123
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="perl"></span>
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124
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ ${AUGUR} filter \</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#f94db01b058d7708a7469ee090e80b78c49de97a"><strong>tests/functional/tree.t</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,6 +29,13 @@ Try building a tree with IQ-TREE using its ModelTest functionality, by supplying</td>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="s1" style="color: #d14;"> > --output "$TMP/tree_raw.nwk" \</span></span>
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30
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="s1" style="color: #d14;"> > --nthreads 1 > /dev/null</span></span>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="s1" style="color: #d14;">Build a tree with excluded sites using a compressed input file.</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"><span class="s1" style="color: #d14;"> $ ${AUGUR} tree \</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"><span class="s1" style="color: #d14;"> > --alignment tree/aligned.fasta.xz \</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"><span class="s1" style="color: #d14;"> > --exclude-sites tree/excluded_sites.txt \</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"><span class="s1" style="color: #d14;"> > --output "$TMP/tree_raw.nwk" &> /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="s1" style="color: #d14;">Clean up tree log files.</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl"><span class="s1" style="color: #d14;"> $ rm -f tree/*.log</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1000</span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#564f4b49fdb146fa67b8810159ab7e0bac38af39"><strong>tests/test_align.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">@@ -10,6 +10,7 @@ from shlex import quote</td>
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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;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span></span>
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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;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MutableSeq</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;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>
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<pre style="margin: 0;"> <span id="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;">augur</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">align</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">@@ -227,13 +228,13 @@ class TestAlign:</td>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_sequences</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="LC230" class="line" lang="python"> <span class="n" style="color: #333;">data_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pathlib</span><span class="p">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="s" style="color: #d14;">'tests/data/align/test_aligned_sequences.fasta'</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;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">read_sequences</span><span class="p">(</span><span class="n" style="color: #333;">data_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">read_sequences</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data_file</span><span class="p">)<span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_seq_compare</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="LC235" class="line" lang="python"> <span class="n" style="color: #333;">data_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pathlib</span><span class="p">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/data/align/aa-seq_h3n2_ha_2y_2HA1_dup.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">AlignmentError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">read_sequences</span><span class="p">(</span><span class="n" style="color: #333;">data_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">read_sequences</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data_file</span><span class="p">)<span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_prepare_no_alignment_or_ref</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">test_file</span><span class="p">,</span> <span class="n" style="color: #333;">test_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">prepare</span><span class="p">([</span><span class="n" style="color: #333;">test_file</span><span class="p">,],</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -366,7 +367,7 @@ class TestAlign:</td>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_postprocess_strip_non_reference</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">ref_file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="s" style="color: #d14;">"""Postprocess should strip gaps in the reference sequence from other sequences, but not gaps in those sequences"""</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">expected_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ref_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">gapped_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ref_seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tomutable</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">gapped_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">MutableSeq</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ref_seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">gapped_seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">gapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">gapped_seq</span><span class="p">,</span> <span class="s" style="color: #d14;">"GAP"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">gap_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_strains</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"gaps"</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">gapped</span><span class="p">])</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/commit/f4634e10ff1048fe07822ced3de385cdd0ca6913#47c96e41e8cfc9b910c0903dca88ffe995e68bb8"><strong>tests/test_filter_groupby.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC2" 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="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">augur.filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">,</span> <span class="n" style="color: #333;">FilterException</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">valid_metadata</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'strain'</span><span class="p">,</span> <span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="s" style="color: #d14;">'country'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_1"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-01-XX"</span><span class="p">,</span><span class="s" style="color: #d14;">"A"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-02-01"</span><span class="p">,</span><span class="s" style="color: #d14;">"A"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_3"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-03-01"</span><span class="p">,</span><span class="s" style="color: #d14;">"B"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_4"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-04-01"</span><span class="p">,</span><span class="s" style="color: #d14;">"B"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_5"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-05-01"</span><span class="p">,</span><span class="s" style="color: #d14;">"B"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">.</span><span class="n" style="color: #333;">from_records</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">).</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'strain'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFilterGroupBy</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_strain_subset</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</span><span class="p">,),</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</span><span class="p">,),</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</span><span class="p">,)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_dummy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</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;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</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="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</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;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</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;">'SEQ_2'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</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;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</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;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</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;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'_dummy'</span><span class="p">,)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_invalid_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</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;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'invalid'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</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;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FilterException</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e_info</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e_info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"The specified group-by categories (['invalid']) were not found. No sequences-per-group sampling will be done."</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_invalid_warn</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">,</span> <span class="n" style="color: #333;">capsys</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'invalid'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_2'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">),</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">),</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">captured</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">capsys</span><span class="p">.</span><span class="n" style="color: #333;">readouterr</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">captured</span><span class="p">.</span><span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"WARNING: Some of the specified group-by categories couldn't be found: invalid</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Filtering by group may behave differently than expected!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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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_groupby_skip_ambiguous_year</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"XXXX-02-01"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</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="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)),</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)),</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)),</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_skip_missing_date</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)),</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</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="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_skip_ambiguous_month</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-XX-01"</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)),</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">3</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="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">4</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="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_skip_missing_month</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020"</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;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</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="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</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;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</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="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</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="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">}]</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_missing_year_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</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;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'year'</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;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">(</span><span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></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;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FilterException</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e_info</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;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</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;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e_info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"The specified group-by categories (['year']) were not found. No sequences-per-group sampling will be done. Note that using 'year' or 'year month' requires a column called 'date'."</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_missing_month_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</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="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">(</span><span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</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;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FilterException</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e_info</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="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e_info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"The specified group-by categories (['month']) were not found. No sequences-per-group sampling will be done. Note that using 'year' or 'year month' requires a column called 'date'."</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_missing_year_and_month_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</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;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">(</span><span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FilterException</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e_info</span><span class="p">:</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e_info</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"The specified group-by categories (['year', 'month']) were not found. No sequences-per-group sampling will be done. Note that using 'year' or 'year month' requires a column called 'date'."</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_missing_date_warn</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">,</span> <span class="n" style="color: #333;">capsys</span><span class="p">):</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">(</span><span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</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="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</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;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</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="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</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="s" style="color: #d14;">'SEQ_2'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</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="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">),</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">),</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unknown'</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="p">}</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">captured</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">capsys</span><span class="p">.</span><span class="n" style="color: #333;">readouterr</span><span class="p">()</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">captured</span><span class="p">.</span><span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"WARNING: A 'date' column could not be found to group-by year or month.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Filtering by group may behave differently than expected!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</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>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_no_strains</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</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;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">]</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{}</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</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>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_only_year_provided</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">]</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'date'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2020'</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</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="s" style="color: #d14;">'SEQ_2'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</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="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</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="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">),</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="p">}</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_month_with_only_year_provided</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</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="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</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;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'date'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2020'</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="p">{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</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="p">{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</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="p">{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</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="p">{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="p">{</span><span class="s" style="color: #d14;">'strain'</span><span class="p">:</span> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter'</span><span class="p">:</span> <span class="s" style="color: #d14;">'skip_group_by_with_ambiguous_month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'kwargs'</span><span class="p">:</span> <span class="s" style="color: #d14;">''</span><span class="p">}</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_groupby_only_year_month_provided</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'country'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</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="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_metadata</span><span class="p">.</span><span class="n" style="color: #333;">copy</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="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'date'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2020-01'</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">tolist</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;">group_by_strain</span><span class="p">,</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_groups_for_subsampling</span><span class="p">(</span><span class="n" style="color: #333;">strains</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">group_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">group_by_strain</span> <span class="o" style="font-weight: 600;">==</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="s" style="color: #d14;">'SEQ_1'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)),</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_2'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</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="LC212" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_3'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</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="LC213" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_4'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</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="LC214" class="line" lang="python"> <span class="s" style="color: #d14;">'SEQ_5'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="mi" style="color: #099;">2020</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">2020</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="LC215" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">skipped_strains</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span></pre>
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