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<h3>
Saira Hussain pushed to branch master
at <a href="https://salsa.debian.org/med-team/epcr">Debian Med / epcr</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/epcr/commit/1656bb9c79685bc69a538bddf597dd4e1afc8674">1656bb9c</a></strong>
<div>
<span>by Saira Hussain</span>
<i>at 2019-06-27T10:20:04Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rename gingo to the proper scientific name gingko
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#1db3a5f5988010349917f2e73750277887baff68">
debian/tests/data/gingo.fasta
→
debian/tests/data/gingko.fasta
</a>
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<li class="file-stats">
<a href="#b98b47746e825f316e6385c892df089913d295dc">
debian/tests/fetch_test_data.py
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="1db3a5f5988010349917f2e73750277887baff68">
<a href="https://salsa.debian.org/med-team/epcr/commit/1656bb9c79685bc69a538bddf597dd4e1afc8674#1db3a5f5988010349917f2e73750277887baff68"><strong>debian/tests/data/gingo.fasta</strong>
→
<strong>debian/tests/data/gingko.fasta</strong>
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<a href="https://salsa.debian.org/med-team/epcr/commit/1656bb9c79685bc69a538bddf597dd4e1afc8674#b98b47746e825f316e6385c892df089913d295dc"><strong>debian/tests/fetch_test_data.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,7 @@ from Bio import Entrez</td>
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6
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">Entrez</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'unknown@debian.org'</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">database</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'nucleotide'</span></span>
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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'data/gingo.fasta'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'data/ging<span class="idiff left right">k</span>o.fasta'</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">'((chloroplast OR plastid) AND "complete genome" AND Embryophyta NOT (mi- tochondrion OR mitochondrial)) AND "Ginkgo biloba"'</span></span>
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<a href="https://salsa.debian.org/med-team/epcr/commit/1656bb9c79685bc69a538bddf597dd4e1afc8674#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,4 +16,7 @@ cd "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell">re-PCR <span class="nt" style="color: #000080;">-S</span> ginko.hash <span class="nt" style="color: #000080;">-n</span> 5 <span class="nt" style="color: #000080;">-g</span> 0 <span class="nt" style="color: #000080;">-d</span> 100-300 <span class="nt" style="color: #000080;">-o</span> rbcL5.rePCR rbcL-primer.txt</span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">famap <span class="nt" style="color: #000080;">-b</span> gingko.mmap <span class="nt" style="color: #000080;">-t</span> N gingko.fasta</span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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="LC21" class="line" lang="shell">fahash <span class="nt" style="color: #000080;">-b</span> gingko.hash <span class="nt" style="color: #000080;">-w</span> 3 <span class="nt" style="color: #000080;">-f</span> 2 gingko.mmap</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">re-PCR <span class="nt" style="color: #000080;">-S</span> gingko.hash <span class="nt" style="color: #000080;">-n</span> 5 <span class="nt" style="color: #000080;">-g</span> 0 <span class="nt" style="color: #000080;">-d</span> 100-300 <span class="nt" style="color: #000080;">-o</span> rbcL5.rePCR rbcL-primer.txt</span></pre>
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