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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pyfaidx">Debian Med / python-pyfaidx</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/96d9c2abe6188a06882a6a1552f9a52b41cc2529">96d9c2ab</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-04-21T14:11:28+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.5.9.5</pre>
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<h4>2 changed files:</h4>
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<a href="#83b1dda3455005121b48aadc1fefedc1b5e999ea">
pyfaidx/__init__.py
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<li class="file-stats">
<a href="#acca83fee2a805bc9377545bfbdbd21c69d727ac">
pyfaidx/cli.py
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<h4>Changes:</h4>
<li id="83b1dda3455005121b48aadc1fefedc1b5e999ea">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/96d9c2abe6188a06882a6a1552f9a52b41cc2529#83b1dda3455005121b48aadc1fefedc1b5e999ea"><strong>pyfaidx/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@ if sys.version_info > (3, ):</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">dna_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.5.9.<span class="idiff left right">2</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">'0.5.9.<span class="idiff left right">5</span>'</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>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">KeyFunctionError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<li id="acca83fee2a805bc9377545bfbdbd21c69d727ac">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/96d9c2abe6188a06882a6a1552f9a52b41cc2529#acca83fee2a805bc9377545bfbdbd21c69d727ac"><strong>pyfaidx/cli.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" 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="126" 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">@@ -126,13 +126,13 @@ def transform_sequence(args, fasta, name, start=None, end=None):</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">transform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'nucleotide'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">).</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">nucs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">([(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">s<span class="idiff left">tr</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff">)</span>.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nb" style="color: #0086b3;">s<span class="idiff">tr</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ss</span></span><span class="p"><span class="idiff right">)</span>)])</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">([(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s<span class="idiff left">s</span></span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">s<span class="idiff right">s</span></span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'T'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">C</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">G</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'N'</span><span class="p">,</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="n" style="color: #333;">others</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'|'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">':'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">v</span></span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()])</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">others</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'|'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">':'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff right">)</span>))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nucs</span><span class="p">.</span><span class="n" style="color: #333;">items</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 class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'{sname}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{sstart}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{send}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{A}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{T}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{C}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{G}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{N}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{others}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sname</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sstart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">send</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">())</span></span>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">transform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'transposed'</span><span class="p">:</span></span>
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138
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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;">return</span> <span class="s" style="color: #d14;">'{name}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{start}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{end}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{seq}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span></span>
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