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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:
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<strong><a href="https://salsa.debian.org/med-team/epcr/commit/bf488007d0ef797e1bac0bbf228025ca4c9167bd">bf488007</a></strong>
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<span>by Saira Hussain</span>
<i>at 2019-06-27T09:45:07Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refactor the fetching script to fetch all the data
Rename and refactor the fasta fetching script in order to fetch
all the data and save them in the right directore
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<h4>1 changed file:</h4>
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<a href="#cb7792c174dbaa287d5801725766d6291db32607">
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−
debian/tests/fetch_fasta.py
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<h4>Changes:</h4>
<li id="cb7792c174dbaa287d5801725766d6291db32607">
<a href="https://salsa.debian.org/med-team/epcr/commit/bf488007d0ef797e1bac0bbf228025ca4c9167bd#cb7792c174dbaa287d5801725766d6291db32607"><strong>debian/tests/fetch_fasta.py</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Entrez</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="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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<pre style="margin: 0;">-<span id="LC6" 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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<pre style="margin: 0;">-<span id="LC7" 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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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" 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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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Fetch the query IDs</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Entrez</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">esearch</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="n" style="color: #333;">term</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Entrez</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'IdList'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Fetch the first result</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="n" style="color: #333;">ff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">handle_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Entrez</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">efetch</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">rettype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">retmode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">handle_fasta</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">()</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>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">handle_fasta</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span></pre>
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