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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-types">Debian Med / q2-types</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/c2e50340431028b3f89595bd8a59de14b15c1c70">c2e50340</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T08:37:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/8a6ed0d9ac2792e1bd6404401b5cb15a82f613d1">8a6ed0d9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T08:37:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2019.7.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/83e00b8cfce412645011d26c23f3adec723b4779">83e00b8c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T08:37:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2019.7.0'
Update to upstream version '2019.7.0'
with Debian dir 08592128bafebe64ffd1b73091d9c7a6d4bcebbf</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/1b7a4d73158f105ecbd5e7065ede8699c4244e30">1b7a4d73</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T08:37:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/ad007ef2706c5a2723d0546ca0c738436dcab9d8">ad007ef2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T08:38:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/043e3c3e6149ab075ccd3d7a3f407cdebd039d02">043e3c3e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T08:38:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/a153552bba2e7aadb3a989420f297f69e932a888">a153552b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T08:42:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#22fbe0b68848772d4b1c45f0d62dcd71a06cde00">
ci/recipe/meta.yaml
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#3bdb7a362f11686a5969dba0363ea115e0751fcb">
q2_types/_version.py
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<li class="file-stats">
<a href="#54ba626fe0572adcddeae8122c558ea2c9f70278">
q2_types/feature_data/__init__.py
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<li class="file-stats">
<a href="#07e3ee9f5c6e5e8399ca48e3a21c5188f5c2f3ea">
q2_types/feature_data/_format.py
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<li class="file-stats">
<a href="#5bfd5c187b0d7270fa753eb3022bb7e84bc92757">
q2_types/feature_data/_transformer.py
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<a href="#5e2e452cb76505dfb05d5e48375d42b44ccee529">
q2_types/feature_data/_type.py
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<li class="file-stats">
<a href="#2f64d23153e4c78cf3c479d1ccf393589c30d55b">
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q2_types/feature_data/tests/data/bad_differential.tsv
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<a href="#ffb5ac1acff245f047beb6cafc44d093a686d5b3">
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q2_types/feature_data/tests/data/differentials.tsv
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q2_types/feature_data/tests/data/dna-sequences-consecutive-ids.fasta
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<li class="file-stats">
<a href="#75f52faf4b672cde309f4c4219361bfe5ed42409">
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q2_types/feature_data/tests/data/dna-sequences-corrupt-characters.fasta
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<a href="#bd4271df3f8ecb27b1b3fdf686c7ef78e8323046">
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q2_types/feature_data/tests/data/dna-sequences-first-line-not-id.fasta
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<a href="#dc5cc846765a14516a5bf6d949b82eecd4c1d8f9">
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q2_types/feature_data/tests/data/dna-with-bom-fails.fasta
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<a href="#e1f8168a828dfcb216831d9c57859b50dc70da7d">
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q2_types/feature_data/tests/data/dna-with-bom-passes.fasta
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<li class="file-stats">
<a href="#4d41a2a9895782f7d19f95b682c401cffcf4885a">
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q2_types/feature_data/tests/data/empty_differential.tsv
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<a href="#fe48c34dfde6481c2b16fc5ead2b9ec1cb6271ab">
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q2_types/feature_data/tests/data/inf_differential.tsv
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<a href="#a7e2c4b4a3d4486b558cf5f957bb4b98777e920e">
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q2_types/feature_data/tests/data/not_differential.tsv
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<li class="file-stats">
<a href="#d4d307c78282f0799835165b31908aff985c5dcd">
q2_types/feature_data/tests/test_format.py
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<li class="file-stats">
<a href="#87c86e89872868b749899f3aac32b2d48779f964">
q2_types/feature_data/tests/test_transformer.py
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<li class="file-stats">
<a href="#951fbd18d3c7980e1c2205bd545ba49a298c39ec">
q2_types/feature_data/tests/test_type.py
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<li class="file-stats">
<a href="#5ff0a0f6759a48f54314c0842863b891bc6ccf3f">
q2_types/feature_table/_transformer.py
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<li class="file-stats">
<a href="#8f30afcf36b530b03db9f722be289872ca2decc1">
q2_types/feature_table/tests/test_transformer.py
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</ul>
<h4>Changes:</h4>
<li id="22fbe0b68848772d4b1c45f0d62dcd71a06cde00">
<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#22fbe0b68848772d4b1c45f0d62dcd71a06cde00"><strong>ci/recipe/meta.yaml</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,8 +21,6 @@ requirements:</td>
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<td class="diff-line-num old_line" data-linenumber="21" 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">
21
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">scikit-bio >=0.5.4</span></span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">numpy</span></span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">blas=*=openblas</span></span>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="24" 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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<td class="diff-line-num new_line old" data-linenumber="24" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># AVX 512 extensions are broken in 0.3.5 and 0.3.6</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="25" 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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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">openblas 0.3.3</span></span>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandas</span></span>
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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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;">biom-format >=2.1.5,<2.2.0</span></span>
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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ijson</span></span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-types (2019.7.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 05 Sep 2019 10:38:27 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">q2-types (2019.4.1-1) unstable; urgency=medium</span>
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2
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Source</span><span class="p">:</span> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">science</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Priority</span><span class="p">:</span> <span class="n" style="color: #333;">optional</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Maintainer</span><span class="p">:</span> <span class="n" style="color: #333;">Debian</span> <span class="n" style="color: #333;">Med</span> <span class="n" style="color: #333;">Packaging</span> <span class="n" style="color: #333;">Team</span> <span class="p"><</span><span class="n" style="color: #333;">debian</span><span class="p">-</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">packaging</span><span class="p">@</span><span class="n" style="color: #333;">lists</span><span class="p">.</span><span class="n" style="color: #333;">alioth</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Liubov</span> <span class="n" style="color: #333;">Chuprikova</span> <span class="p"><</span><span class="n" style="color: #333;">chuprikovalv</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</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="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span> <span class="p">(>=</span> <span class="m" style="color: #099;">12</span><span class="p">~),</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">science</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Priority</span><span class="p">:</span> <span class="n" style="color: #333;">optional</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span><span class="p">-</span><span class="n" style="color: #333;">compat</span> <span class="p">(=</span> <span class="m" style="color: #099;">12</span><span class="p">),</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">dh</span><span class="p">-</span><span class="n" style="color: #333;">python</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">setuptools</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">@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 12~),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">ijson</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">h5py</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.<span class="idiff left right">3</span>.0</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.<span class="idiff left right">4</span>.0</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span></span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -14,7 +14,9 @@ export PYBUILD_BEFORE_INSTALL=rm -rvf {build_dir}/q2-types.egg-* {build_dir}/sit</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_types"</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_install</span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#3bdb7a362f11686a5969dba0363ea115e0751fcb"><strong>q2_types/_version.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,9 +23,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 2019.<span class="idiff left right">4.1</span>)"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">39051b2475fccf77526778589b67efcbf00314cf</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-0<span class="idiff left right">5-08 16:49:19 -07</span>00"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 2019.<span class="idiff left right">7.0</span>)"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">9f31de0c81510fbe6be8b16f95e23b4c974ca002</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-0<span class="idiff left right">7-30 18:15:54 +00</span>00"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#54ba626fe0572adcddeae8122c558ea2c9f70278"><strong>q2_types/feature_data/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +13,11 @@ from ._format import (</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">HeaderlessTSVTaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">TSVTaxonomyFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedDNAFASTAFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">)</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;">._type</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">FeatureData</span><span class="p">,</span> <span class="n" style="color: #333;">Taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndSequence</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedSequence</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;">FeatureData</span><span class="p">,</span> <span class="n" style="color: #333;">Taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndSequence</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedSequence</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;">Differential</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># TODO remove these imports when tests are rewritten. Remove from __all__ too</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._transformer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DNAIterator</span><span class="p">,</span> <span class="n" style="color: #333;">PairedDNAIterator</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedDNAIterator</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,11 +25,11 @@ from ._transformer import DNAIterator, PairedDNAIterator, AlignedDNAIterator</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'TaxonomyFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TaxonomyDirectoryFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'HeaderlessTSVTaxonomyFormat'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'HeaderlessTSVTaxonomyDirectoryFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TSVTaxonomyFormat'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'TSVTaxonomyDirectoryFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DNAFASTAFormat'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'TSVTaxonomyDirectoryFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DNAFASTAFormat'</span><span class="p">,</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'DifferentialFormat'</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'DNASequencesDirectoryFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PairedDNASequencesDirectoryFormat'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">'AlignedDNAFASTAFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AlignedDNASequencesDirectoryFormat'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'FeatureData'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Taxonomy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Sequence'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PairedEndSequence'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'AlignedSequence'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DNAIterator'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PairedDNAIterator'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'AlignedDNAIterator'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'AlignedDNAIterator'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'Differential'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'DifferentialDirectoryFormat'</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="n" style="color: #333;">importlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'q2_types.feature_data._transformer'</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#07e3ee9f5c6e5e8399ca48e3a21c5188f5c2f3ea"><strong>q2_types/feature_data/_format.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,8 +6,12 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</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;">skbio.io</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2.plugin.model</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">model</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;">qiime2.plugin</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ValidationError</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</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;">..plugin_setup</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">plugin</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,23 +135,47 @@ TSVTaxonomyDirectoryFormat = model.SingleFileDirectoryFormat(</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DNAFASTAFormat</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TextFileFormat</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sniff</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="LC135" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">sniffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skbio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">io_registry</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sniffer</span><span class="p">(</span><span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sniffer</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">generator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skbio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">constructor</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">skbio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DNA</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">verify</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC140" 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="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</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="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ValueError raised by skbio if there are invalid DNA chars.</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_lines</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">max_lines</span><span class="p">):</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">FASTADNAValidator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'[ACGTURYKMSWBDHVN]+\r?\n?'</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;">last_line_was_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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147
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141
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<pre style="margin: 0;"> <span id="LC141" 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="c1" style="color: #998; font-style: italic;"># Empty files are ok also</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;">empty_sniffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skbio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">io_registry</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sniffer</span><span class="p">(</span><span class="s" style="color: #d14;">'<emptyfile>'</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">empty_sniffer</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">),</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first</span><span class="p">[:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\xEF\xBB\xBF</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">:]</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Empty files should validate</span></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;">if</span> <span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">''</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="k" style="font-weight: 600;">return</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">'>'</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="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="s" style="color: #d14;">"First line of file is not a valid "</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="s" style="color: #d14;">"FASTA ID. FASTA IDs must start "</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">"with '>'"</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="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line_number</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line_number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_lines</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8-sig'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_line_was_ID</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="s" style="color: #d14;">'Multiple consecutive IDs '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="s" style="color: #d14;">'starting on line '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'{line_number-1!r}'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">last_line_was_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fullmatch</span><span class="p">(</span><span class="n" style="color: #333;">FASTADNAValidator</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">last_line_was_ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="s" style="color: #d14;">'Invalid characters on line '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'{line_number} (does not match '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">'IUPAC characters for a DNA '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">'sequence).'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">UnicodeDecodeError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'utf-8 cannot decode byte on line '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'{line_number}'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">e</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">max_lines</span><span class="p">):</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">level_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'min'</span><span class="p">:</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="s" style="color: #d14;">'max'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">'inf'</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_validate_lines</span><span class="p">(</span><span class="n" style="color: #333;">level_map</span><span class="p">[</span><span class="n" style="color: #333;">max_lines</span><span class="p">])</span></span>
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151
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"></span>
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152
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"></span>
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153
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"><span class="n" style="color: #333;">DNASequencesDirectoryFormat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SingleFileDirectoryFormat</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -185,10 +213,30 @@ AlignedDNASequencesDirectoryFormat = model.SingleFileDirectoryFormat(</td>
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185
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNAFASTAFormat</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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187
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DifferentialFormat</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TextFileFormat</span><span class="p">):</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" 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="LC219" class="line" lang="python"> <span class="n" style="color: #333;">md</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">))</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MetadataFileError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">md_exc</span><span class="p">:</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="n" style="color: #333;">md_exc</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">md_exc</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">md</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="224" 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">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="s" style="color: #d14;">'Format must contain at least 1 column'</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">filtered_md</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">md</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter_columns</span><span class="p">(</span><span class="n" style="color: #333;">column_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'numeric'</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filtered_md</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_count</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">md</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">column_count</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="s" style="color: #d14;">'Must only contain numeric values.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"><span class="n" style="color: #333;">DifferentialDirectoryFormat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SingleFileDirectoryFormat</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="s" style="color: #d14;">'DifferentialDirectoryFormat'</span><span class="p">,</span> <span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">,</span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"></span>
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_formats</span><span class="p">(</span></span>
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">TSVTaxonomyFormat</span><span class="p">,</span> <span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</span><span class="p">,</span></span>
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190
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">HeaderlessTSVTaxonomyFormat</span><span class="p">,</span> <span class="n" style="color: #333;">HeaderlessTSVTaxonomyDirectoryFormat</span><span class="p">,</span></span>
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">TaxonomyFormat</span><span class="p">,</span> <span class="n" style="color: #333;">TaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">DNASequencesDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</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;">AlignedDNAFASTAFormat</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNAFASTAFormat</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span></span>
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#5bfd5c187b0d7270fa753eb3022bb7e84bc92757"><strong>q2_types/feature_data/_transformer.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ from ..plugin_setup import plugin</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..feature_table</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BIOMV210Format</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">TaxonomyFormat</span><span class="p">,</span> <span class="n" style="color: #333;">HeaderlessTSVTaxonomyFormat</span><span class="p">,</span> <span class="n" style="color: #333;">TSVTaxonomyFormat</span><span class="p">,</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">,</span> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</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;">AlignedDNAFASTAFormat</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;">AlignedDNAFASTAFormat</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">DifferentialFormat</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Taxonomy format transformers</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">@@ -359,3 +359,21 @@ def _19(data: AlignedDNAIterator) -> AlignedDNAFASTAFormat:</td>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_33</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">:</span> <span class="n" style="color: #333;">AlignedDNAFASTAFormat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_dnafastaformats_to_metadata</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># differential types</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_222</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">:</span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_223</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">:</span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_224</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">ff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">qiime2</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;">data</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">save</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ff</span></span></pre>
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<li id="5e2e452cb76505dfb05d5e48375d42b44ccee529">
<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#5e2e452cb76505dfb05d5e48375d42b44ccee529"><strong>q2_types/feature_data/_type.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,8 @@ from qiime2.plugin import SemanticType</td>
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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;">..plugin_setup</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">plugin</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;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">DifferentialDirectoryFormat</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>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">FeatureData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SemanticType</span><span class="p">(</span><span class="s" style="color: #d14;">'FeatureData'</span><span class="p">,</span> <span class="n" style="color: #333;">field_names</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'type'</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">@@ -26,8 +27,13 @@ PairedEndSequence = SemanticType('PairedEndSequence',</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">AlignedSequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SemanticType</span><span class="p">(</span><span class="s" style="color: #d14;">'AlignedSequence'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">variant_of</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FeatureData</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">field</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">Differential</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SemanticType</span><span class="p">(</span><span class="s" style="color: #d14;">'Differential'</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;">variant_of</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FeatureData</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">field</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_semantic_types</span><span class="p">(</span><span class="n" style="color: #333;">FeatureData</span><span class="p">,</span> <span class="n" style="color: #333;">Taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">PairedEndSequence</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedSequence</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">PairedEndSequence</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedSequence</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">Differential</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_semantic_type_to_format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">FeatureData</span><span class="p">[</span><span class="n" style="color: #333;">Taxonomy</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">@@ -41,3 +47,5 @@ plugin.register_semantic_type_to_format(</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_semantic_type_to_format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">FeatureData</span><span class="p">[</span><span class="n" style="color: #333;">AlignedSequence</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">artifact_format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_semantic_type_to_format</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;">FeatureData</span><span class="p">[</span><span class="n" style="color: #333;">Differential</span><span class="p">],</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#2f64d23153e4c78cf3c479d1ccf393589c30d55b"><strong>q2_types/feature_data/tests/data/bad_differential.tsv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">featureid effect bad_effect</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">F0 -0.910182258821735 a</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">F1 1.01418002973925 0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">F2 1.02456128258909 0</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">F3 -0.74363992043225 0</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">F4 1.29823896534823 0</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">F28 -0.31799033232181 0</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">F29 -0.66141741897569 0</span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#ffb5ac1acff245f047beb6cafc44d093a686d5b3"><strong>q2_types/feature_data/tests/data/differentials.tsv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">featureid effect</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">F0 -0.910182258821735</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">F1 1.01418002973925</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">F2 1.02456128258909</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">F3 -0.74363992043225</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">F4 1.29823896534823</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">F5 -1.12965055281585</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">F6 -0.522401797448688</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">F7 0.327560711072239</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">F8 -1.3738693465664802</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">F9 -0.7847891526325621</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">F10 -0.280063201878434</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">F11 -0.251269847578052</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">F12 1.24602780723028</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">F13 0.665734866338239</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">F14 -0.889042985114811</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">F15 -0.811956802515126</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">F16 0.11591764582945001</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">F17 -0.156195990858492</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">F18 -0.965770633683909</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">F19 0.8035240337800391</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">F20 0.680306950765235</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">F21 -0.688388077896823</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">F22 0.7949653982850671</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">F23 -1.11912925367142</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">F24 -1.1059356352774599</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">F25 0.678934047810573</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">F26 -0.937189288219405</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">F27 -0.9997301931164799</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">F28 -0.31799033232181</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">F29 -0.66141741897569</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">F30 0.550511528315366</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#40d1833188fc9513cbd7c2da855648e1004c3f8d"><strong>q2_types/feature_data/tests/data/dna-sequences-consecutive-ids.fasta</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>This is an ID</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">>This is another ID</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#75f52faf4b672cde309f4c4219361bfe5ed42409"><strong>q2_types/feature_data/tests/data/dna-sequences-corrupt-characters.fasta</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>This data is corrupt</span></pre>
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<pre style="margin: 0;">+</pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#bd4271df3f8ecb27b1b3fdf686c7ef78e8323046"><strong>q2_types/feature_data/tests/data/dna-sequences-first-line-not-id.fasta</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">This is not an id</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#dc5cc846765a14516a5bf6d949b82eecd4c1d8f9"><strong>q2_types/feature_data/tests/data/dna-with-bom-fails.fasta</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Not a valid id</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#e1f8168a828dfcb216831d9c57859b50dc70da7d"><strong>q2_types/feature_data/tests/data/dna-with-bom-passes.fasta</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>Some kinda DNA</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ACGTACGTACGT</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#4d41a2a9895782f7d19f95b682c401cffcf4885a"><strong>q2_types/feature_data/tests/data/empty_differential.tsv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">featureid</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">F0</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">F1</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">F2</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">F3</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">F4</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">F5</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">F6</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">F7</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">F8</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">F9</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">F10</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">F11</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">F12</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">F13</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">F14</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">F15</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">F16</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">F17</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">F18</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">F19</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">F20</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">F21</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">F22</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">F23</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">F24</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">F25</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">F26</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">F27</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">F28</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">F29</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">F30</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#fe48c34dfde6481c2b16fc5ead2b9ec1cb6271ab"><strong>q2_types/feature_data/tests/data/inf_differential.tsv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">featureid effect</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">F0 inf</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">F1 1.01418002973925</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">F2 1.02456128258909</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">F3 -0.74363992043225</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">F4 1.29823896534823</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">F5 -1.12965055281585</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">F6 -0.522401797448688</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">F7 0.327560711072239</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">F8 -1.3738693465664802</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">F9 -0.7847891526325621</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">F10 -0.280063201878434</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">F11 -0.251269847578052</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">F12 1.24602780723028</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">F13 0.665734866338239</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">F14 -0.889042985114811</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">F15 -0.811956802515126</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">F16 0.11591764582945</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">F17 -0.156195990858492</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">F18 -0.965770633683909</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">F19 0.8035240337800391</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">F20 0.680306950765235</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">F21 -0.688388077896823</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">F22 0.7949653982850671</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">F23 -1.11912925367142</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">F24 -1.10593563527746</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">F25 0.678934047810573</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">F26 -0.937189288219405</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">F27 -0.99973019311648</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">F28 -0.31799033232181</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">F29 -0.66141741897569</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">F30 0.550511528315366</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#a7e2c4b4a3d4486b558cf5f957bb4b98777e920e"><strong>q2_types/feature_data/tests/data/not_differential.tsv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">asdfasdfasdfasdf asdfasdfa asdfasdf asdf asdfas dfa</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#d4d307c78282f0799835165b31908aff985c5dcd"><strong>q2_types/feature_data/tests/test_format.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">@@ -16,7 +16,7 @@ from q2_types.feature_data import (</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">HeaderlessTSVTaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">TSVTaxonomyFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedDNAFASTAFormat</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;">AlignedDNASequencesDirectoryFormat</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">DifferentialDirectoryFormat</span></span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.plugin.testing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestPluginBase</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.plugin</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ValidationError</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,12 +144,11 @@ class TestDNAFASTAFormats(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_<span class="idiff left right">validate_negative</span></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="LC148" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">not-dna-sequences</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_<span class="idiff left right">bom_passes</span></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="LC148" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">dna-with-bom-passes.fasta</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'DNAFASTA'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_empty_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'empty'</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">@@ -159,6 +158,41 @@ class TestDNAFASTAFormats(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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161
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_validate_negative</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'not-dna-sequences'</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'DNAFASTA'</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="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</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>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_consecutive_IDs</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'dna-sequences-consecutive-ids.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'consecutive IDs.*1'</span><span class="p">):</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</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>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_missing_initial_ID</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'dna-sequences-first-line-not-id.fasta'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'First line'</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="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</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>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_corrupt_characters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'dna-sequences-corrupt-characters.fasta'</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="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'utf-8.*2'</span><span class="p">):</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_fasta_format_bom_fails</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'dna-with-bom-fails.fasta'</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="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'First line'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"></span>
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162
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_dna_sequences_directory_format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'dna-sequences.fasta'</span><span class="p">)</span></span>
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164
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">filepath</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">@@ -203,5 +237,58 @@ class TestDNAFASTAFormats(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</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>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestDifferentialFormat</span><span class="p">(</span><span class="n" style="color: #333;">TestPluginBase</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">package</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'q2_types.feature_data.tests'</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_format</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="LC244" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_format_empty</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'empty_differential.tsv'</span><span class="p">)</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">))</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'least 1 column'</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_format_not</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'not_differential.tsv'</span><span class="p">)</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">))</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">):</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_format_inf</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="LC273" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'inf_differential.tsv'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">))</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'numeric'</span><span class="p">):</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_format_bad_type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'bad_differential.tsv'</span><span class="p">)</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">))</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'numeric'</span><span class="p">):</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">(</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">()</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"></span>
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206
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#87c86e89872868b749899f3aac32b2d48779f964"><strong>q2_types/feature_data/tests/test_transformer.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">@@ -21,7 +21,7 @@ from q2_types.feature_data import (</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">TaxonomyFormat</span><span class="p">,</span> <span class="n" style="color: #333;">HeaderlessTSVTaxonomyFormat</span><span class="p">,</span> <span class="n" style="color: #333;">TSVTaxonomyFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNAIterator</span><span class="p">,</span> <span class="n" style="color: #333;">PairedDNAIterator</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedDNAFASTAFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNAIterator</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">DifferentialFormat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">AlignedDNAIterator</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_types.feature_data._transformer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">_taxonomy_formats_to_dataframe</span><span class="p">,</span> <span class="n" style="color: #333;">_dataframe_to_tsv_taxonomy_format</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">@@ -656,5 +656,42 @@ class TestDNAFASTAFormatTransformers(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">exp</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestDifferentialTransformer</span><span class="p">(</span><span class="n" style="color: #333;">TestPluginBase</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"> <span class="n" style="color: #333;">package</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'q2_types.feature_data.tests'</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_to_df</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="LC663" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transform_format</span><span class="p">(</span><span class="n" style="color: #333;">DifferentialFormat</span><span class="p">,</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sniff to see if the first 4 feature ids are the same</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'F0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F3'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</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="LC670" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertListEqual</span><span class="p">(</span><span class="n" style="color: #333;">exp</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_to_md</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="LC673" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transform_format</span><span class="p">(</span><span class="n" style="color: #333;">DifferentialFormat</span><span class="p">,</span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'differentials.tsv'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sniff to see if the first 4 feature ids are the same</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'F0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'F3'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</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="LC680" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertListEqual</span><span class="p">(</span><span class="n" style="color: #333;">exp</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_df_to_differential</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="LC683" class="line" lang="python"> <span class="n" style="color: #333;">transformer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_transformer</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">,</span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Index</span><span class="p">([</span><span class="s" style="color: #d14;">'SEQUENCE1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SEQUENCE2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SEQUENCE3'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'featureid'</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python"> <span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.3</span><span class="p">,</span> <span class="mf" style="color: #099;">0.1</span><span class="p">,</span> <span class="mf" style="color: #099;">1.2</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;">index</span><span class="p">,</span> <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;">'differential'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transformer</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIsInstance</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">DifferentialFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python"> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#951fbd18d3c7980e1c2205bd545ba49a298c39ec"><strong>q2_types/feature_data/tests/test_type.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">@@ -10,8 +10,9 @@ import unittest</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_types.feature_data</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">FeatureData</span><span class="p">,</span> <span class="n" style="color: #333;">Taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndSequence</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedSequence</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">Differential</span><span class="p">,</span> <span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">DNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">,</span> <span class="n" style="color: #333;">PairedDNASequencesDirectoryFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">AlignedDNASequencesDirectoryFormat</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.plugin.testing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestPluginBase</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,6 +35,13 @@ class TestTypes(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_aligned_sequence_semantic_type_registration</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRegisteredSemanticType</span><span class="p">(</span><span class="n" style="color: #333;">AlignedSequence</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_semantic_type_registration</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRegisteredSemanticType</span><span class="p">(</span><span class="n" style="color: #333;">AlignedSequence</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_differential_semantic_type_to_format_registration</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertSemanticTypeRegisteredToFormat</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;">FeatureData</span><span class="p">[</span><span class="n" style="color: #333;">Differential</span><span class="p">],</span> <span class="n" style="color: #333;">DifferentialDirectoryFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_taxonomy_semantic_type_to_format_registration</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="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertSemanticTypeRegisteredToFormat</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;">FeatureData</span><span class="p">[</span><span class="n" style="color: #333;">Taxonomy</span><span class="p">],</span> <span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#5ff0a0f6759a48f54314c0842863b891bc6ccf3f"><strong>q2_types/feature_table/_transformer.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">@@ -73,13 +73,6 @@ def _table_to_v210(data):</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ff</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_table_to_v100</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">ff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BIOMV100Format</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_json</span><span class="p">(</span><span class="n" style="color: #333;">generated_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_get_generated_by</span><span class="p">(),</span> <span class="n" style="color: #333;">direct_io</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fh</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ff</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_dataframe_to_table</span><span class="p">(</span><span class="n" style="color: #333;">df</span><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;">if</span> <span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inferred_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'string'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Please provide a DataFrame with a string-based Index"</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">@@ -87,16 +80,6 @@ def _dataframe_to_table(df):</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">sample_ids</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_1</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">:</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Table</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">BIOMV100Format</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_drop_axis_metadata</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">ff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BIOMV100Format</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</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;">fh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_json</span><span class="p">(</span><span class="n" style="color: #333;">generated_by</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_get_generated_by</span><span class="p">()))</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ff</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_2</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">:</span> <span class="n" style="color: #333;">BIOMV100Format</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Table</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;">return</span> <span class="n" style="color: #333;">_parse_biom_table_v100</span><span class="p">(</span><span class="n" style="color: #333;">ff</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">@@ -152,12 +135,6 @@ def _10(df: pd.DataFrame) -> BIOMV210Format:</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_table_to_v210</span><span class="p">(</span><span class="n" style="color: #333;">_dataframe_to_table</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_11</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">:</span> <span class="n" style="color: #333;">BIOMV210Format</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">BIOMV100Format</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_parse_biom_table_v210</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_table_to_v100</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">plugin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register_transformer</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_12</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">:</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Table</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">qiime2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Metadata</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_table_to_metadata</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<li id="8f30afcf36b530b03db9f722be289872ca2decc1">
<a href="https://salsa.debian.org/med-team/q2-types/compare/afa40c46951c3023897821090e77cf9a3c686f36...a153552bba2e7aadb3a989420f297f69e932a888#8f30afcf36b530b03db9f722be289872ca2decc1"><strong>q2_types/feature_table/tests/test_transformer.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,20 +24,6 @@ from q2_types.feature_table._transformer import (_parse_biom_table_v100,</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestTransformers</span><span class="p">(</span><span class="n" style="color: #333;">TestPluginBase</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">package</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'q2_types.feature_table.tests'</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_biom_table_to_biom_v100_format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'feature-table_v100.biom'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">transformer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_transformer</span><span class="p">(</span><span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Table</span><span class="p">,</span> <span class="n" style="color: #333;">BIOMV100Format</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_table</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transformer</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_table</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">input</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'observation'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'observation'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'sample'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'sample'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_biom_v100_format_to_biom_table</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transform_format</span><span class="p">(</span><span class="n" style="color: #333;">BIOMV100Format</span><span class="p">,</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Table</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'feature-table_v100.biom'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -111,17 +97,6 @@ class TestTransformers(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'sample'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</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;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'sample'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_biom_v210_format_to_biom_v100_format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transform_format</span><span class="p">(</span><span class="n" style="color: #333;">BIOMV210Format</span><span class="p">,</span> <span class="n" style="color: #333;">BIOMV100Format</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'feature-table_v210.biom'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_table</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_table</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">))</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'observation'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'observation'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'sample'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</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;">'sample'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">())</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"></span>
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125
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_to_pandas_data_frame_to_biom_v210_format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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126
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'feature-table_v100.biom'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">transformer1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_transformer</span><span class="p">(</span><span class="n" style="color: #333;">BIOMV100Format</span><span class="p">,</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span></span>
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