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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-cgecore">Debian Med / python-cgecore</a>
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<h4>
Commits:
</h4>
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<strong><a href="https://salsa.debian.org/med-team/python-cgecore/-/commit/9875aef4619fd85db0d3cd23c25cc2c5a47b5df9">9875aef4</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-11-27T22:43:01+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.6+ds</pre>
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<h4>3 changed files:</h4>
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<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#99e6b3e9b6332ede61f0c761ad90306a89039e05">
cgecore/__init__.py
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<li class="file-stats">
<a href="#81293046cfcd19d3582f14835e080d2d680f9865">
cgecore/blaster/blaster.py
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<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/python-cgecore/-/commit/9875aef4619fd85db0d3cd23c25cc2c5a47b5df9#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.0</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: cgecore</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.5.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.5.<span class="idiff left right">6</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Center for Genomic Epidemiology Core Module</span>
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<td class="diff-line-num old_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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<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="plaintext">Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module</span>
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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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Center for Genomic Epidemiology</span>
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<li id="99e6b3e9b6332ede61f0c761ad90306a89039e05">
<a href="https://salsa.debian.org/med-team/python-cgecore/-/commit/9875aef4619fd85db0d3cd23c25cc2c5a47b5df9#99e6b3e9b6332ede61f0c761ad90306a89039e05"><strong>cgecore/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" 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="13" 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">@@ -13,7 +13,7 @@ from .argumentparsing import (check_file_type, get_arguments, get_string,</td>
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<td class="diff-line-num old_line" data-linenumber="13" 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="LC13" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#####################</span></span>
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<pre style="margin: 0;">-<span id="LC16" 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;">"1.5.<span class="idiff left right">5</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC16" 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;">"1.5.<span class="idiff left right">6</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"argumentparsing"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="19" 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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"cmdline"</span><span class="p">,</span></span>
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<li id="81293046cfcd19d3582f14835e080d2d680f9865">
<a href="https://salsa.debian.org/med-team/python-cgecore/-/commit/9875aef4619fd85db0d3cd23c25cc2c5a47b5df9#81293046cfcd19d3582f14835e080d2d680f9865"><strong>cgecore/blaster/blaster.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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="46" 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">@@ -46,9 +46,9 @@ class Blaster():</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Found "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" skipping DB."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">b''</span><span class="p">,</span> <span class="s" style="color: #d14;">b''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC48" 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="LC49" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"%s -subject %s -query %s -out %s -outfmt <span class="idiff left right">'5'</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"%s -subject %s -query %s -out %s -outfmt <span class="idiff left right">5</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">" -perc_identity %s -max_target_seqs %s"</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">" -dust <span class="idiff left right">'no'</span>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">blast</span><span class="p">,</span> <span class="n" style="color: #333;">db_file</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">" -dust <span class="idiff left right">no</span>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">blast</span><span class="p">,</span> <span class="n" style="color: #333;">db_file</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="n" style="color: #333;">max_target_seqs</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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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