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<h3>
Liubov Chuprikova 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/043a6cd7bc6818c3424d077b00a6949e847c6e17">043a6cd7</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2019-12-15T12:43:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2019.10.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/dc01841d082472287e93639ef7effba8735d873e">dc01841d</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2019-12-15T12:43:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2019.10.0'
Update to upstream version '2019.10.0'
with Debian dir 4ea41af5a920871301db43c3ea2eabf61fff4117</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/a77a552cb1f3c21c02edac27d39177cabcba6d2c">a77a552c</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2019-12-15T12:45:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
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<h4>20 changed files:</h4>
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<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="#3bdb7a362f11686a5969dba0363ea115e0751fcb">
q2_types/_version.py
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<li class="file-stats">
<a href="#07e3ee9f5c6e5e8399ca48e3a21c5188f5c2f3ea">
q2_types/feature_data/_format.py
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<a href="#5bfd5c187b0d7270fa753eb3022bb7e84bc92757">
q2_types/feature_data/_transformer.py
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q2_types/feature_data/tests/data/dna-sequences-duplicate-id.fasta
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q2_types/feature_data/tests/data/dna-sequences-id-starts-with-space.fasta
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q2_types/feature_data/tests/data/dna-sequences-no-id.fasta
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<a href="#9f6f8c270c74c84717fafe0cd68fb5d635b58f42">
q2_types/feature_data/tests/data/taxonomy/blanks-and-comments
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q2_types/feature_data/tests/data/taxonomy/blanks
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q2_types/feature_data/tests/data/taxonomy/greater-column-length.tsv
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q2_types/feature_data/tests/data/taxonomy/greater-header-length.tsv
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<a href="#9e65e06ed9c5d2e73c12327a69a21e658efe567d">
q2_types/feature_data/tests/data/taxonomy/header-only.tsv
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q2_types/feature_data/tests/data/taxonomy/leading_space_taxon.tsv
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q2_types/feature_data/tests/data/taxonomy/start_end_space_taxon.tsv
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q2_types/feature_data/tests/data/taxonomy/trailing_space_taxon.tsv
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<a href="#d5eac1f70a164e14b20c1648e6fd02cb97fc025b">
q2_types/feature_data/tests/data/taxonomy/valid-but-messy.tsv
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<a href="#d4d307c78282f0799835165b31908aff985c5dcd">
q2_types/feature_data/tests/test_format.py
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<a href="#87c86e89872868b749899f3aac32b2d48779f964">
q2_types/feature_data/tests/test_transformer.py
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<a href="#fee7edd437132b8130e00bd73f4e50a25c852f18">
q2_types/feature_table/_format.py
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<a href="#d29ba8b5a02bb36b7083d6b033a1716d883f9fc0">
q2_types/sample_data/tests/test_transformer.py
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<h4>Changes:</h4>
<li id="22fbe0b68848772d4b1c45f0d62dcd71a06cde00">
<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#22fbe0b68848772d4b1c45f0d62dcd71a06cde00"><strong>ci/recipe/meta.yaml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -25,6 +25,8 @@ requirements:</td>
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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="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="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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<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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<td class="diff-line-num new_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="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">h5py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">matplotlib 3.1.0</span></span>
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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">matplotlib-base 3.1.0</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="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2 {{ release }}.*</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"><span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">q2-types (2019.<span class="idiff left right">7.0-2</span>) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-types (2019.<span class="idiff left right">10.0-1</span>) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Minor changes in autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> <span class="idiff left right">Tue, 17 Sep 2019 12:01:34 +02</span>00</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> <span class="idiff left right">Sun, 15 Dec 2019 13:44:07 +01</span>00</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">q2-types (2019.7.0-1) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#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">7</span>.0)"</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-<span class="idiff left right">07-30 18:15:54</span> +0000"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 2019.<span class="idiff left right">10</span>.0)"</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">b382dd345500fc2172858ff00638e6bca35760ed</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2019-<span class="idiff left right">11-01 01:04:25</span> +0000"</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/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#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">@@ -54,9 +54,6 @@ class TaxonomyFormat(model.TextFileFormat):</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Blank line</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</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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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Comment line</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">cells</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cells</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</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">@@ -93,41 +90,53 @@ class TSVTaxonomyFormat(model.TextFileFormat):</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> Optionally followed by other arbitrary columns.</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> This format supports <span class="idiff left right">comment lines starting with #, and blank lines. The</span></span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">expected header must be the first non-comment, non-blank line. In addition</span></span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">to the header, there must be at least one line </span>of data.</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> This format supports <span class="idiff left right">blank lines. The expected header must be the first</span></span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">non-blank line. In addition to the header, there must be at least one line</span></span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;"> of data.</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">HEADER</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'Feature ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Taxon'</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="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">sniff</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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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;"><span class="idiff left">_check_n_records</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">n</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC101" 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="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="LC105" class="line" lang="python"> <span class="n" style="color: #333;">data_line<span class="idiff left right">s</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">data_line<span class="idiff left right">_count</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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106
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">data_lines</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">line</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;">readline</span><span class="p">()</span></span>
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109
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># EOF</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">file_</span> <span class="o" style="font-weight: 600;">=</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">),</span> <span class="n" style="color: #333;">fh</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">file_</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Tracks line number for error reporting</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" 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;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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114
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Blank line</span></span>
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115
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</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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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Comment line</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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119
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114
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<pre style="margin: 0;"> <span id="LC114" 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="n" style="color: #333;">cells</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;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">cells</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;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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121
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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122
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cells</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</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;">HEADER</span><span class="p">:</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" 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>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s must be the first two header values. The '</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">'first two header values provided are: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (on '</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">'line </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s).'</span> <span class="o" style="font-weight: 600;">%</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;">HEADER</span><span class="p">,</span> <span class="n" style="color: #333;">cells</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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124
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cells</span></span>
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125
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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126
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cells</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">):</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">data_lines</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'Number of values on line </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s are not the same as '</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">'number of header values. Found </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s values '</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'(</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s), expected </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cells</span><span class="p">),</span> <span class="n" style="color: #333;">cells</span><span class="p">,</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="nb" style="color: #0086b3;">len</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;">HEADER</span><span class="p">)))</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">data_line_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data_line_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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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span><span class="s" style="color: #d14;">'No taxonomy records found, only blank '</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="s" style="color: #d14;">'lines and/or a header row.'</span><span class="p">)</span></span>
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129
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">header</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">data_lines</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</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_</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">level</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_check_n_records</span><span class="p">(</span><span class="n" style="color: #333;">n</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;">10</span><span class="p">,</span> <span class="s" style="color: #d14;">'max'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">}[</span><span class="n" style="color: #333;">level</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>
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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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133
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"><span class="n" style="color: #333;">TSVTaxonomyDirectoryFormat</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="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,6 +147,7 @@ class DNAFASTAFormat(model.TextFileFormat):</td>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_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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148
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<pre style="margin: 0;"> <span id="LC148" 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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149
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<pre style="margin: 0;"> <span id="LC149" 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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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141
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>
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142
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152
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<pre style="margin: 0;"> <span id="LC152" 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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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" 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">@@ -149,8 +159,8 @@ class DNAFASTAFormat(model.TextFileFormat):</td>
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149
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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150
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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;">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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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;">"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;">"<span class="idiff left right">FASTA ID. FASTA IDs must star</span>t "</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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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="s" style="color: #d14;">"<span class="idiff left right">description. Descriptions mus</span>t "</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="s" style="color: #d14;">"<span class="idiff left right">start </span>with '>'"</span><span class="p">)</span></span>
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154
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164
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<pre style="margin: 0;"> <span id="LC164" 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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155
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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156
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166
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<pre style="margin: 0;"> <span id="LC166" 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 unfold js-unfold old_line" data-linenumber="158" 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="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -158,9 +168,24 @@ class DNAFASTAFormat(model.TextFileFormat):</td>
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158
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">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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159
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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160
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_line_was_ID</span><span class="p">:</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="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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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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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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171
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<pre style="margin: 0;">+<span id="LC171" 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 '</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">'descriptions starting on '</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'line {line_number-1!r}'</span><span class="p">)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">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;">split</span><span class="p">()</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</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="s" style="color: #d14;">'>'</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="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" 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>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'Description on line {line_number} is '</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">'missing an ID.'</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'ID on line {line_number} starts with a '</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="s" style="color: #d14;">'space. IDs may not start with spaces'</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ids</span><span class="p">:</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ValidationError</span><span class="p">(</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'ID on line {line_number} is a duplicate of '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'another ID on line {ids[line[0]]}.'</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">line</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="n" style="color: #333;">line_number</span></span>
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164
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">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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165
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190
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<pre style="margin: 0;"> <span id="LC190" 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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166
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,7 +47,7 @@ def _taxonomy_formats_to_dataframe(filepath, has_header=None):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Using `dtype=object` and `set_index()` to avoid type casting/inference of</span></span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># any columns or the index.</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">df</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;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">comment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'#'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">skip_blank_lines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">df</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;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">skip_blank_lines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">object</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</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">@@ -88,6 +88,7 @@ def _taxonomy_formats_to_dataframe(filepath, has_header=None):</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">"column names are duplicated: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_duplicates</span><span class="p">()))</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'Taxon'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'Taxon'</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</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="LC1" class="line" lang="plaintext">>SEQUENCE1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>SEQUENCE1</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">ACGTACGTACGTACGTACGTACGT</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">> this_id_starts_with_a_space</span></pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># hello</span>
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4
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"># world #</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># hello, peanut</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">#</span>
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14
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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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15
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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="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></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"> </span>
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17
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#58412b37abdba67332891a8dfec0802b2ef60e83"><strong>q2_types/feature_data/tests/data/taxonomy/greater-column-length.tsv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Feature ID Taxon</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">seq1 k__Bacteria; p__Proteobacteria -1.0</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">seq2 k__Bacteria 1.0</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#1635d050f197c40f1092f0f0cb287c06ed8a5e38"><strong>q2_types/feature_data/tests/data/taxonomy/greater-header-length.tsv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Feature ID Taxon Confidence Random</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">seq1 k__Foo; p__Bar -1.0</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">seq2 k__Foo; p__Baz -42.0</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#9e65e06ed9c5d2e73c12327a69a21e658efe567d"><strong>q2_types/feature_data/tests/data/taxonomy/header-only.tsv</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># This file</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># only has a</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># header!</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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7
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Feature ID Taxon</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#cfd03a0e2aaf218532f58fe07328733b29e97ec5"><strong>q2_types/feature_data/tests/data/taxonomy/leading_space_taxon.tsv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Feature ID Taxon Confidence</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">seq1 k__Foo; p__Bar -1.0</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#86190f51867666de533873d9ae1a5b471621f794"><strong>q2_types/feature_data/tests/data/taxonomy/start_end_space_taxon.tsv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Feature ID Taxon Confidence</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">seq1 k__Foo; p__Bar -1.0</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#e69df51028ea2f989aa3007b4d3d80676eb7be57"><strong>q2_types/feature_data/tests/data/taxonomy/trailing_space_taxon.tsv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Feature ID Taxon Confidence</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">seq1 k__Foo; p__Bar -1.0</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#d5eac1f70a164e14b20c1648e6fd02cb97fc025b"><strong>q2_types/feature_data/tests/data/taxonomy/valid-but-messy.tsv</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># There's some important whitespace in this file for testing, take care not to</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># remove :)</span>
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5
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"># hello</span>
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7
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># world #</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></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">@@ -15,20 +15,20 @@</td>
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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"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"><span class="idiff left right"># comment</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Feature ID Taxon Extra Column</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"># hello, peanut</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"># </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">SEQUENCE1 k__Bar; p__Baz foo</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"><span class="idiff left right"># GWAR</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">seq2 some; taxonomy; for; ya bar baz</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"><span class="idiff left right"># FOOTER</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#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">@@ -37,7 +37,7 @@ class TestTaxonomyFormats(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC37" 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="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_taxonomy_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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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="s" style="color: #d14;">'blanks<span class="idiff left right">-and-comments</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1-column.tsv'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="s" style="color: #d14;">'blanks'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1-column.tsv'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">filepaths</span> <span class="o" style="font-weight: 600;">=</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;">get_data_path</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'taxonomy'</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filenames</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC43" 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">@@ -78,7 +78,7 @@ class TestTaxonomyFormats(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC78" 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="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_headerless_tsv_taxonomy_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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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="s" style="color: #d14;">'blanks<span class="idiff left right">-and-comments</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1-column.tsv'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="s" style="color: #d14;">'blanks'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1-column.tsv'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">filepaths</span> <span class="o" style="font-weight: 600;">=</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;">get_data_path</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'taxonomy'</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filenames</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC84" 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">@@ -113,7 +113,7 @@ class TestTaxonomyFormats(TestPluginBase):</td>
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113
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<pre style="margin: 0;"> <span id="LC113" 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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114
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"></span>
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tsv_taxonomy_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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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="s" style="color: #d14;">'blanks<span class="idiff left right">-and-comments</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1-column.tsv'</span><span class="p">,</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="s" style="color: #d14;">'blanks'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1-column.tsv'</span><span class="p">,</span></span>
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117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">'headerless.tsv'</span><span class="p">,</span> <span class="s" style="color: #d14;">'header-only.tsv'</span><span class="p">,</span> <span class="s" style="color: #d14;">'jagged.tsv'</span><span class="p">]</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">filepaths</span> <span class="o" style="font-weight: 600;">=</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;">get_data_path</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'taxonomy'</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filenames</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">@@ -134,6 +134,19 @@ class TestTaxonomyFormats(TestPluginBase):</td>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>
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135
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<pre style="margin: 0;"> <span id="LC135" 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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136
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tsv_taxonomy_format_column_header_lengths</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'greater-column-length.tsv'</span><span class="p">,</span> <span class="s" style="color: #d14;">'greater-header-length.tsv'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">filepaths</span> <span class="o" style="font-weight: 600;">=</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;">get_data_path</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'taxonomy'</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">))</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filenames</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>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filepath</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filepaths</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC144" 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;">TSVTaxonomyFormat</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="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC146" 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>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">'line 2.*3 values.*expected 2'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC148" 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="LC149" class="line" lang="python"></span>
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150
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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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestDNAFASTAFormats</span><span class="p">(</span><span class="n" style="color: #333;">TestPluginBase</span><span class="p">):</span></span>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" 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="182" 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">@@ -169,7 +182,8 @@ class TestDNAFASTAFormats(TestPluginBase):</td>
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169
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<pre style="margin: 0;"> <span id="LC182" 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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170
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<pre style="margin: 0;"> <span id="LC183" 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="LC184" 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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<pre style="margin: 0;">+<span id="LC185" 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>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'consecutive descriptions.*1'</span><span class="p">):</span></span>
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173
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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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<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_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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" 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="215" 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">@@ -201,6 +215,28 @@ class TestDNAFASTAFormats(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC216" 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="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC218" 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_duplicate_ids</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="LC219" 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-duplicate-id.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC220" 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="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="n" style="color: #333;">ValidationError</span><span class="p">,</span> <span class="s" style="color: #d14;">'3.*duplicate.*1'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC223" 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="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC225" 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_no_id</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="LC226" 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-no-id.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC227" 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="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">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;">'1.*missing an ID'</span><span class="p">):</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" 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="LC231" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC232" 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_id_starts_with_space</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="LC233" 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>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="s" style="color: #d14;">'dna-sequences-id-starts-with-space.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC235" 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="LC236" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC237" 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;">'1 starts with a space'</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="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="LC239" class="line" lang="python"></span>
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204
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_paired_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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205
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241
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<pre style="margin: 0;"> <span id="LC241" 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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206
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242
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<pre style="margin: 0;"> <span id="LC242" 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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<li id="87c86e89872868b749899f3aac32b2d48779f964">
<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#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">@@ -264,6 +264,45 @@ class TestTaxonomyFormatTransformers(TestPluginBase):</td>
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264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"></span>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" 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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266
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tsv_taxonomy_to_metadata_trailing_whitespace_taxon</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" 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;">TSVTaxonomyFormat</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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269
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<pre style="margin: 0;">+<span id="LC269" 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>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="s" style="color: #d14;">'taxonomy'</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 class="s" style="color: #d14;">'trailing_space_taxon.tsv'</span><span class="p">))</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"></span>
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273
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<pre style="margin: 0;">+<span id="LC273" 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;">'seq1'</span><span class="p">],</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Feature ID'</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">object</span><span class="p">)</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">exp_df</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 class="s" style="color: #d14;">'k__Foo; p__Bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-1.0'</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>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'Taxon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Confidence'</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">object</span><span class="p">)</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" 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;">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;">exp_df</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="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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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tsv_taxonomy_to_metadata_leading_whitespace_taxon</span><span class="p">(</span><span class="bp" style="color: #999;">self</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 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;">TSVTaxonomyFormat</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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282
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<pre style="margin: 0;">+<span id="LC282" 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>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="s" style="color: #d14;">'taxonomy'</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="s" style="color: #d14;">'leading_space_taxon.tsv'</span><span class="p">))</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"></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;">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;">'seq1'</span><span class="p">],</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Feature ID'</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">object</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 class="n" style="color: #333;">exp_df</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 class="s" style="color: #d14;">'k__Foo; p__Bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-1.0'</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>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'Taxon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Confidence'</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">object</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="n" style="color: #333;">exp</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 class="n" style="color: #333;">exp_df</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>
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291
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<pre style="margin: 0;">+<span id="LC291" 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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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"></span>
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_tsv_taxonomy_to_metadata_trailing_leading_whitespace_taxon</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" 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;">TSVTaxonomyFormat</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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295
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<pre style="margin: 0;">+<span id="LC295" 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>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="s" style="color: #d14;">'taxonomy'</span><span class="p">,</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="s" style="color: #d14;">'start_end_space_taxon.tsv'</span><span class="p">))</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>
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299
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<pre style="margin: 0;">+<span id="LC299" 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;">'seq1'</span><span class="p">],</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Feature ID'</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">object</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">exp_df</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 class="s" style="color: #d14;">'k__Foo; p__Bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-1.0'</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>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'Taxon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Confidence'</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">object</span><span class="p">)</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" 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;">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;">exp_df</span><span class="p">)</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"></span>
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304
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<pre style="margin: 0;">+<span id="LC304" 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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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"></span>
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># In-depth testing of the `_taxonomy_formats_to_dataframe` helper function,</span></span>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># which does the heavy lifting for the transformers.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="275" 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">@@ -275,11 +314,11 @@ class TestTaxonomyFormatsToDataFrame(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">_taxonomy_formats_to_dataframe</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'taxonomy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1-column.tsv'</span><span class="p">)))</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_blanks<span class="idiff left right">_and_comments</span></span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_blanks</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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318
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<pre style="margin: 0;"> <span id="LC318" 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;">pandas</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;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EmptyDataError</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">_taxonomy_formats_to_dataframe</span><span class="p">(</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="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="s" style="color: #d14;">'taxonomy'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="s" style="color: #d14;">'blanks<span class="idiff left right">-and-comments</span>'</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="s" style="color: #d14;">'blanks'</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_empty</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="LC324" 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;">pandas</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;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EmptyDataError</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#fee7edd437132b8130e00bd73f4e50a25c852f18"><strong>q2_types/feature_table/_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">@@ -22,7 +22,8 @@ class BIOMV100Format(model.TextFileFormat):</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">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="LC25" 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="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="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Can't self.open(mode='rb'), so we defer to the backing pathlib object</span></span>
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<pre style="margin: 0;">+<span id="LC26" 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;">path</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</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;">'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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<pre style="margin: 0;"> <span id="LC27" 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="LC28" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ijson</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">event</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parser</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/21c6a64ea5c4cfa8b452e9c453be6ddbc43de0e4...a77a552cb1f3c21c02edac27d39177cabcba6d2c#d29ba8b5a02bb36b7083d6b033a1716d883f9fc0"><strong>q2_types/sample_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">@@ -26,7 +26,10 @@ class TestTransformers(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'shannon'</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;">exp_index</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" 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="n" style="color: #333;">exp</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;">obs</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;">Series</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_csv</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 class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Squeeze equals true to return series instead of dataframe</span></span>
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<pre style="margin: 0;">+<span id="LC31" 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;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_csv</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 class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">squeeze</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">assert_series_equal</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="LC35" class="line" lang="python"></span>
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