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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/ragout">Debian Med / ragout</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/6a1d30496b8334b33c598c8c0f3b796eeb90b88c">6a1d3049</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2020-01-04T19:23:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More stable clean. Another Python3 issue.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/b49f737499be4a61e66fbed6f0d26385f971f5f6">b49f7374</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2020-01-04T19:27:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dfsg -> ds
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/f8d2ee67757b5d97770a5f3589d44a2eaaac403d">f8d2ee67</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2020-01-04T19:37:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added d/gbp.conf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/9c222fd000295dbf25fb2756261a7dfcd3bdfa2b">9c222fd0</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2020-01-04T19:38:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">It is a team-upload
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#67df3adc98b97f87d2c73e4a05f22a987c3a5a7b">
<span class="new-file">
+
debian/gbp.conf
</span>
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ragout/compare/c8991daa17bb287539836c822f77dfe48368fe61...9c222fd000295dbf25fb2756261a7dfcd3bdfa2b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ragout (2.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ragout (2.2+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [Andreas Tille]</span>
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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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" 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">@@ -10,12 +12,15 @@ ragout (2.2-1) unstable; urgency=medium</td>
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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> * Not having Python install binaries in setup.py, chaning</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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="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="plaintext"> d/ragout.install accordingly</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * bin/ragout was still about to invoke python2</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * maketrans is now a static function of str</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * not allowing bin/ragout to change $PATH </span>
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> * demoted sibelia to recommends runtime dependency as there are</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> modules that don't use it.</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> TODO: Find out what happened to</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> https://salsa.debian.org/med-team/sibelia</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC21" class="line" lang="plaintext"> which is not in new or main.</span>
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<td class="diff-line-num new new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> * use "ds" not "dfsg" as version suffix since files were removed</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> but no functional changes have been performed.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sat, 04 Jan 2020 19:07:58 +0100</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/ragout/compare/c8991daa17bb287539836c822f77dfe48368fe61...9c222fd000295dbf25fb2756261a7dfcd3bdfa2b#67df3adc98b97f87d2c73e4a05f22a987c3a5a7b"><strong>debian/gbp.conf</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="conf">[<span class="n" style="color: #333;">import</span>-<span class="n" style="color: #333;">orig</span>]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="conf"><span class="n" style="color: #333;">pristine</span>-<span class="n" style="color: #333;">tar</span> = <span class="n" style="color: #333;">True</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="conf"></span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/c8991daa17bb287539836c822f77dfe48368fe61...9c222fd000295dbf25fb2756261a7dfcd3bdfa2b#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</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">@@ -422,10 +422,10 @@ Index: ragout/ragout/main.py</td>
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#import synteny_backend.cactus</span></span>
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import synteny_backend.maf</span></span>
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import synteny_backend.hal</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from synteny_backend import sibelia</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from <span class="idiff left right">ragout.</span>synteny_backend import sibelia</span></span>
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#from synteny_backend import cactus</span></span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from synteny_backend import maf</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from synteny_backend import hal</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from <span class="idiff left right">ragout.</span>synteny_backend import maf</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from <span class="idiff left right">ragout.</span>synteny_backend import hal</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="diff"> logger = logging.getLogger()</span>
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431
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="diff"> debugger = DebugConfig.get_instance()</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1269" 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>
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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">@@ -1269,3 +1269,27 @@ Index: ragout/bin/ragout</td>
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1269
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1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="diff"> #Ragout entry point</span>
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1270
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1270
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<pre style="margin: 0;"> <span id="LC1270" class="line" lang="diff"> from ragout.main import main</span>
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1271
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1271
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<pre style="margin: 0;"> <span id="LC1271" class="line" lang="diff"> sys.exit(main())</span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/parsers/fasta_parser.py</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1274" 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">
1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/parsers/fasta_parser.py</span></span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/parsers/fasta_parser.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1276" 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">
1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="diff"><span class="p">@@ -8,8 +8,6 @@</span> This module provides some basic FASTA I/</span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="diff"> </span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="diff"> import logging</span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="diff"> </span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from string import maketrans</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="diff"> logger = logging.getLogger()</span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="diff"> </span>
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1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="diff"> class FastaError(Exception):</span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="diff"><span class="p">@@ -61,8 +59,8 @@</span> def write_fasta_dict(fasta_dict, filenam</span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="diff"> f.write(fasta_dict[header][i:i + 60] + "\n")</span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="diff"> </span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="diff"> </span>
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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-COMPL = maketrans("ATGCURYKMSWBVDHNXatgcurykmswbvdhnx",</span></span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "TACGAYRMKSWVBHDNXtacgayrmkswvbhdnx")</span></span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+COMPL = str.maketrans("ATGCURYKMSWBVDHNXatgcurykmswbvdhnx",</span></span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "TACGAYRMKSWVBHDNXtacgayrmkswvbhdnx")</span></span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="diff"> def reverse_complement(string):</span>
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1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="diff"> return string[::-1].translate(COMPL)</span>
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1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="diff"> </span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/ragout/compare/c8991daa17bb287539836c822f77dfe48368fe61...9c222fd000295dbf25fb2756261a7dfcd3bdfa2b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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>
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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">@@ -15,7 +15,7 @@ override_dh_install:</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> find debian -name LICENSE -delete</span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> dh_auto_clean</span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_auto_clean<span class="idiff left right"> || true</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">
19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> rm -f bin/ragout-maf2synteny bin/ragout-overlap</span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> rm -rf .pybuild</span>
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<td class="diff-line-num old_line" data-linenumber="21" 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">
21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> find . -name "*.o" -delete</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/c8991daa17bb287539836c822f77dfe48368fe61...9c222fd000295dbf25fb2756261a7dfcd3bdfa2b#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+d<span class="idiff left right">fsg</span>,dversionmangle=auto,repack,compression=xz" \</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+d<span class="idiff left right">s</span>,dversionmangle=auto,repack,compression=xz" \</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> https://github.com/fenderglass/Ragout/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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