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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/fastaq">Debian Med / fastaq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastaq/commit/e4dd7b7f6d4f01fc0b193e609338be560d7e3bb8">e4dd7b7f</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-02-22T10:22:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.17.0</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#48d2f0efc4b0d484ae7dbc868d3f14512cbce66d">
pyfastaq/sequences.py
</a>
</li>
<li class="file-stats">
<a href="#856672c263ad1692eb41d8e00952446439a87b46">
pyfastaq/tests/sequences_test.py
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="48d2f0efc4b0d484ae7dbc868d3f14512cbce66d">
<a href="https://salsa.debian.org/med-team/fastaq/commit/e4dd7b7f6d4f01fc0b193e609338be560d7e3bb8#48d2f0efc4b0d484ae7dbc868d3f14512cbce66d"><strong>pyfastaq/sequences.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">string</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfastaq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">utils</span><span class="p">,</span> <span class="n" style="color: #333;">intervals</span><span class="p">,</span> <span class="n" style="color: #333;">genetic_codes</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Error</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span> <span class="k" style="font-weight: 600;">pass</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">@@ -465,6 +464,47 @@ class Fasta:</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python">        <span class="s" style="color: #d14;">'''Returns a Fasta sequence, translated into amino acids. Starts translating from 'frame', where frame expected to be 0,1 or 2'''</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <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;">genetic_codes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">codes</span><span class="p">[</span><span class="n" style="color: #333;">genetic_code</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</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;">seq</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">(),</span> <span class="s" style="color: #d14;">'X'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)]))</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gc_content</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">as_decimal</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="LC468" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns the GC content for the sequence.</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"><span class="s" style="color: #d14;">        Notes:</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"><span class="s" style="color: #d14;">            This method ignores N when calculating the length of the sequence.</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"><span class="s" style="color: #d14;">            It does not, however ignore other ambiguous bases. It also only</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"><span class="s" style="color: #d14;">            includes the ambiguous base S (G or C). In this sense the method is</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"><span class="s" style="color: #d14;">            conservative with its calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"><span class="s" style="color: #d14;">            as_decimal (bool): Return the result as a decimal. Setting to False</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"><span class="s" style="color: #d14;">            will return as a percentage. i.e for the sequence GCAT it will</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"><span class="s" style="color: #d14;">            return 0.5 by default and 50.00 if set to False.</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"><span class="s" style="color: #d14;">        Returns:</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"><span class="s" style="color: #d14;">            float: GC content calculated as the number of G, C, and S divided</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"><span class="s" style="color: #d14;">            by the number of (non-N) bases (length).</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python">        <span class="n" style="color: #333;">gc_total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python">        <span class="n" style="color: #333;">num_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python">        <span class="n" style="color: #333;">n_tuple</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="s" style="color: #d14;">'nN'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python">        <span class="n" style="color: #333;">accepted_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="s" style="color: #d14;">'cCgGsS'</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="489" 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">
489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="468" 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="490" 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">
490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># counter sums all unique characters in sequence. Case insensitive.</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="491" 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">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Counter</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;">seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="492" 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">
492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="493" 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">
493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># dont count N in the number of bases</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="494" 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">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">base</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">n_tuple</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="495" 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">
495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python">                <span class="n" style="color: #333;">num_bases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="496" 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">
496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="468" 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="497" 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">
497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">base</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">accepted_bases</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># S is a G or C</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="498" 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">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python">                    <span class="n" style="color: #333;">gc_total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="499" 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">
499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="500" 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">
500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python">        <span class="n" style="color: #333;">gc_content</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gc_total</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">num_bases</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="501" 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">
501
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="502" 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">
502
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC502" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">as_decimal</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># return as percentage</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="503" 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">
503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python">            <span class="n" style="color: #333;">gc_content</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">100</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="504" 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">
504
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"></span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="468" 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="505" 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">
505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gc_content</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="468" 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="506" 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">
506
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"></span>
</pre>
</td>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Embl</span><span class="p">(</span><span class="n" style="color: #333;">Fasta</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python">    <span class="s" style="color: #d14;">'''Exactly the same as Fasta, but reading seqs from a file works differently'''</span></span>
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<br>
</li>
<li id="856672c263ad1692eb41d8e00952446439a87b46">
<a href="https://salsa.debian.org/med-team/fastaq/commit/e4dd7b7f6d4f01fc0b193e609338be560d7e3bb8#856672c263ad1692eb41d8e00952446439a87b46"><strong>pyfastaq/tests/sequences_test.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">@@ -520,6 +520,19 @@ class TestFasta(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python">            <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python">            <span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split_capillary_id</span><span class="p">()</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_gc_content</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 new new_line" data-linenumber="524" 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="LC524" class="line" lang="python">        <span class="s" style="color: #d14;">"""Test GC content calculation works as expected"""</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python">        <span class="n" style="color: #333;">tests</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<td class="diff-line-num new new_line" data-linenumber="526" 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="LC526" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cgCG'</span><span class="p">),</span> <span class="mf" style="color: #099;">1.0</span><span class="p">),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="523" 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="527" 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">
527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tTaA'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="523" 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="528" 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">
528
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC528" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCAT'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.5</span><span class="p">),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="523" 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="529" 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">
529
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC529" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCATNN'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.5</span><span class="p">),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="523" 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="530" 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">
530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCATNNS'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.6</span><span class="p">),</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="523" 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="531" 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">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCATNNSK'</span><span class="p">),</span> <span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="532" 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">
532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python">        <span class="p">]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="533" 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">
533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">test</span><span class="p">,</span> <span class="n" style="color: #333;">answer</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tests</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="523" 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="534" 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">
534
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<pre style="margin: 0;">+<span id="LC534" 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;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gc_content</span><span class="p">(),</span> <span class="n" style="color: #333;">answer</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="535" 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">
535
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<pre style="margin: 0;">+<span id="LC535" 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;">assertAlmostEqual</span><span class="p">(</span><span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gc_content</span><span class="p">(</span><span class="n" style="color: #333;">as_decimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">),</span> <span class="n" style="color: #333;">answer</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
</pre>
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523
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="524" 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">
524
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestEmbl</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
</pre>
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525
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_id_from_header_line</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
</pre>
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<br>
</li>
<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/fastaq/commit/e4dd7b7f6d4f01fc0b193e609338be560d7e3bb8#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,7 +4,7 @@ from setuptools import setup, find_packages</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
</pre>
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5
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
</pre>
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<td class="diff-line-num old_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="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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" 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;">'pyfastaq'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7" 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">
7
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<td class="diff-line-num new_line old" data-linenumber="7" 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="LC7" class="line" lang="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'3.1<span class="idiff left right">6</span>.0'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="8" 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="7" 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">
7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'3.1<span class="idiff left right">7</span>.0'</span><span class="p">,</span></span>
</pre>
</td>
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<td class="diff-line-num old_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">
8
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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">
8
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="python">    <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Script to manipulate FASTA and FASTQ files, plus API for developers'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
</pre>
</td>
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<td class="diff-line-num old_line" data-linenumber="10" 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">
10
</td>
<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Martin Hunt'</span><span class="p">,</span></span>
</pre>
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