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<h3>

Étienne Mollier pushed to branch master

at <a href="https://salsa.debian.org/med-team/seqmagick">Debian Med / seqmagick</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/4e3793b35bb4593681f8c5fbbd7005063aae7d50">4e3793b3</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T19:36:55+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add myself to uploaders

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/e01a38e1942bc323edd4d95cd3f3a3b64a7c614c">e01a38e1</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T19:37:21+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/3e36ac3bf6d53643ba93cafda0481629d1b4b6c3">3e36ac3b</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T19:37:22+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.2</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/b6abab8bdce080521450fdc10faa63cc361577db">b6abab8b</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T19:37:24+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.8.2'

Update to upstream version '0.8.2'

with Debian dir 2c8672eab4a6d0b10461170278df9dc6ac62c415</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/70126746b0e25b184367c4adb5e56372b6c1b7ae">70126746</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T19:59:15+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove fix-myfunctions-example-file.patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/9f30150d646e0c82a3234700384528a81070567d">9f30150d</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T19:59:56+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove replace-biopython-trie-with-pygtrie.patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/d553b0242cce10e71ce63e417ab1d3e44850d485">d553b024</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T20:00:19+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">refresh biopython_1.71_dual_coding_support.patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/b1226a0fdf31ce0accc4f265efc64ecc200bbbcd">b1226a0f</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T20:00:33+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update patch series

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/43cda2641bbf9dfb0bb9c40c8931f10fbf166f9e">43cda264</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T20:00:54+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/seqmagick/-/commit/304ee0448f44a2eea0867205f97fab1f82dbbe24">304ee044</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2020-11-14T20:02:02+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>25 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#561b88e19de321ca62c7590bbb350765fb110905">

README.rst

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#dc8a19de74e4a49ad03b0e604379d9f3df20da62">

debian/patches/biopython_1.71_dual_coding_support.patch

</a>

</li>

<li class="file-stats">

<a href="#490a82a2fa527c129de4e49174e3ee693da72117">

<span class="deleted-file">

−

debian/patches/fix-myfunctions-example-file.patch

</span>

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</li>

<li class="file-stats">

<a href="#0ddc2310a98e93221ce234f9be58d879d176994a">

<span class="deleted-file">

−

debian/patches/replace-biopython-trie-with-pygtrie.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#b3bea44a8f91e14f357ec4e44fced1bde9f0fc6f">

docs/changelog.rst

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<li class="file-stats">

<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">

docs/index.rst

</a>

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<li class="file-stats">

<a href="#df6ef13e0e421ccbeb52ae3dafc71163e05f4a2b">

examples/apply-function/myfunctions.py

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</li>

<li class="file-stats">

<a href="#d5b95025744fd1556a32320b8f795fd339151809">

requirements-rtd.txt

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</li>

<li class="file-stats">

<a href="#19359a61ae2446b51b549167b014da2fcf265768">

requirements.txt

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<li class="file-stats">

<a href="#91aa5d4c72a3b7266c11a0eec9925cdd76b3b800">

seqmagick/subcommands/convert.py

</a>

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<li class="file-stats">

<a href="#7aa62f8d9518716248903b7c8bb9a36c457a3b62">

seqmagick/subcommands/primer_trim.py

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<li class="file-stats">

<a href="#6a735fce2f4ff0f1995bdadd69efeeb9f2ac3fc8">

seqmagick/subcommands/quality_filter.py

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<li class="file-stats">

<a href="#0650a49d4ac15d63dd5695c48a2badeb9d925786">

<span class="new-file">

+

seqmagick/test/integration/data/input6.fasta

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</a>

</li>

<li class="file-stats">

<a href="#66391cb3b0062ee21bb22d56cf718d57a54d50b0">

seqmagick/test/integration/data/output2.nex

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<li class="file-stats">

<a href="#8b40d397823d5340dc6f6114c84cd6a1d967026c">

<span class="new-file">

+

seqmagick/test/integration/data/output3.nex

</span>

</a>

</li>

<li class="file-stats">

<a href="#ef3896f5c1c77ea6efce689d9c056c1c4f28f8c3">

<span class="new-file">

+

seqmagick/test/integration/data/output4.nex

</span>

</a>

</li>

<li class="file-stats">

<a href="#82e1c6c9831266d85ede6ec0e472a68670a2054a">

seqmagick/test/integration/test_convert.py

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<li class="file-stats">

<a href="#f12631b6aa2f26ba5d46a706cbddc73a139cbeb6">

seqmagick/test/test_primer_trim.py

</a>

</li>

<li class="file-stats">

<a href="#f52b658e1d9f644a85f4f9e6d945e49f85814b46">

seqmagick/test/test_subcommands_quality_filter.py

</a>

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<li class="file-stats">

<a href="#00abf6d2722a5596aed9abe31af5e5146fe97133">

seqmagick/test/test_transform.py

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<li class="file-stats">

<a href="#87b1ac486a071802f654fab8fafaa5df5e186b8b">

seqmagick/transform.py

</a>

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</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,7 +3,7 @@ python:</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># - "2.7"</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num 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">

4

</td>

<td class="diff-line-num 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">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># - "pypy"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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

</td>

<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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># - "3.4"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6" 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">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="6" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>- "3.5"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7" 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">

7

</td>

<td class="diff-line-num new_line" data-linenumber="7" 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">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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

</td>

<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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<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

</td>

<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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_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="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">@@ -12,7 +12,7 @@ python:</td>

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<td class="diff-line-num old_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">

12

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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="yaml"><span class="c1" style="color: #998; font-style: italic;"># BioPython doesn't always play well with pip install.</span></span>

</pre>

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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">

13

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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="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old_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">

14

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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="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">if</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">[[</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">$TRAVIS_PYTHON_VERSION</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">!=</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">'pypy'</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">]];</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">then</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-q</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">numpy;</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">fi"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

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<td class="diff-line-num new_line old" data-linenumber="15" 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="LC15" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-q</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">biopython</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">nose"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" 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="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="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-q</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">biopython</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">nose</span><span class="nv" style="color: #008080;"><span class="idiff left"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">pygtrie</span>"</span></span>

</pre>

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<td class="diff-line-num old_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">

16

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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="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">."</span></span>

</pre>

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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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<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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"></span>

</pre>

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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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<td class="diff-line-num new_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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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</table>

<br>

</li>

<li id="561b88e19de321ca62c7590bbb350765fb110905">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ there is one that takes arguments::</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Requirements</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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="LC20" class="line" lang="plaintext">============</span>

</pre>

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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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC22" class="line" lang="plaintext">* Python >= 3.<span class="idiff left right">4</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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="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">* Python >= 3.<span class="idiff left right">5</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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="23" 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="LC23" class="line" lang="plaintext">* biopython >= 1.70</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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="24" 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="LC24" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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="25" 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="LC25" class="line" lang="plaintext">Installation</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="29" 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">@@ -29,7 +29,7 @@ Use pip::</td>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>

</pre>

</td>

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30

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<td class="diff-line-num new_line" data-linenumber="30" 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">

30

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">   pip install seqmagick</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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">

31

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<td class="diff-line-num new_line" data-linenumber="31" 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">

31

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num new_line old" data-linenumber="32" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">Note that as of version 0.<span class="idiff left right">7.0, this package requires Python 3.4</span>+. If</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="33" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Note that as of version 0.<span class="idiff left right">8.0, this package requires Python 3.5</span>+. If</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="33" 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">

33

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<td class="diff-line-num new_line" data-linenumber="33" 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">

33

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">you want to use the most recent version compatible with Python 2.7::</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" 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">

34

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<td class="diff-line-num new_line" data-linenumber="34" 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">

34

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" 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">

35

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<td class="diff-line-num new_line" data-linenumber="35" 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">

35

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">  pip install seqmagick==0.6.2</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="1" 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="1" 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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seqmagick (0.8.2-1) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="2" 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">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="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">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Add myself to Uploaders.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="4" 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">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Refresh patches:</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">    - remove fix-myfunctions-example-file.patch, applied upstream;</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">    - remove replace-biopython-trie-with-pygtrie.patch, applied upstream;</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">    - refresh biopython_1.71_dual_coding_support.patch hunks.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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="9" 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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org>  Sat, 14 Nov 2020 20:01:17 +0100</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="11" 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">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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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">

12

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">seqmagick (0.8.0-2) unstable; urgency=medium</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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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">

13

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

</td>

<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">

14

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">  * Team Upload.</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: seqmagick</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">           Étienne Mollier <etienne.mollier@mailoo.org></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>

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</li>

<li id="dc8a19de74e4a49ad03b0e604379d9f3df20da62">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#dc8a19de74e4a49ad03b0e604379d9f3df20da62"><strong>debian/patches/biopython_1.71_dual_coding_support.patch</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,11 +17,9 @@ forwarding this to the wrapped forward table.</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> seqmagick/transform.py | 4 ++++</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> 1 file changed, 4 insertions(+)</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff">Index: seqmagick/seqmagick/transform.py</span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff">--- seqmagick.orig/seqmagick/transform.py</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ seqmagick/seqmagick/transform.py</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -67<span class="idiff left">3,6 +673,10 @@</span></span><span class="idiff right"> class CodonWarningTable(object):</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -67<span class="idiff left right">0,6 +670,10 @@</span></span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff">         return value in self.wrapped</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>

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<br>

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<li id="490a82a2fa527c129de4e49174e3ee693da72117">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#490a82a2fa527c129de4e49174e3ee693da72117"><strong>debian/patches/fix-myfunctions-example-file.patch</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Nilesh Patra <npatra974@gmail.com></span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: Encode hash result in hash_starts_numeric to support unicode</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/fhcrc/seqmagick/pull/85</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last Changed: August 16, 2020</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/examples/apply-function/myfunctions.py</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/examples/apply-function/myfunctions.py</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -14,6 +14,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">     their sha-1 hash.</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">     """</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">     for record in records:</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        seq_hash = hashlib.sha1(str(record.seq)).hexdigest()</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        seq_hash = hashlib.sha1(str(record.seq).encode('utf-8')).hexdigest()</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">         if seq_hash[0].isdigit():</span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">             yield record</span></pre>

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<br>

</li>

<li id="0ddc2310a98e93221ce234f9be58d879d176994a">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#0ddc2310a98e93221ce234f9be58d879d176994a"><strong>debian/patches/replace-biopython-trie-with-pygtrie.patch</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Nilesh Patra <npatra974@gmail.com></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: Replace deprecated Biopython trie functionality with  pygtrie</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/fhcrc/seqmagick/pull/86</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Changed: August 16, 2020</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqmagick/subcommands/quality_filter.py</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqmagick/subcommands/quality_filter.py</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="0" 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="diff"><span class="p">@@ -11,16 +11,29 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC8" class="line" lang="diff"> import time</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC9" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC10" class="line" lang="diff"> from Bio import SeqIO</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-try:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    from Bio import trie, triefind</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-except ImportError:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    trie = None</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    triefind = None</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pygtrie as trie</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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">

17

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC17" class="line" lang="diff"> from Bio.SeqIO import QualityIO</span>

</pre>

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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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC18" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC19" class="line" lang="diff"> from seqmagick import fileformat, __version__</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC20" class="line" lang="diff"> from .common import typed_range, FileType</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="21" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="23" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def trie_match(string, trie):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="24" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    def has_prefix(teststring, trie):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for key in trie.keys():</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if key.startswith(teststring):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" 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="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                return True</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        return False</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    longest = None</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" 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="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for i in range(len(string)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        substr = string[:i + 1]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" 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="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if not has_prefix(substr, trie):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            break</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" 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="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if trie.has_key(substr):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" 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="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            longest = substr</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" 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="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return longest</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC39" class="line" lang="diff"> # Default minimummean quality score</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" 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="LC40" class="line" lang="diff"> DEFAULT_MEAN_SCORE = 25.0</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" 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="LC41" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" 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="LC42" class="line" lang="diff"><span class="p">@@ -626,7 +639,7 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff">         self.trie = trie</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" 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="LC44" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" 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="LC45" class="line" lang="diff">     def filter_record(self, record):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" 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="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        m = triefind.match(str(record.seq), self.trie)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        m = trie_match(str(record.seq), self.trie)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff">         if m:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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="LC49" class="line" lang="diff">             if self.listener:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" 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="LC50" class="line" lang="diff">                 self.listener(</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" 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="LC51" class="line" lang="diff"><span class="p">@@ -646,7 +659,7 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" 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="LC52" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" 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="LC53" class="line" lang="diff">     Any additional columns are ignored</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" 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="LC54" class="line" lang="diff">     """</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" 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="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    tr = trie.trie()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    tr = trie.StringTrie()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" 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="LC57" class="line" lang="diff">     reader = csv.reader(fp)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" 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="LC59" class="line" lang="diff">     if header:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" 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="LC60" class="line" lang="diff"><span class="p">@@ -680,10 +693,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff">         raise ValueError("--quality-window-mean-qual specified without "</span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff">                          "--quality-window")</span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    if trie is None or triefind is None:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" 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="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        raise ValueError(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="66" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            'Missing Bio.trie and/or Bio.triefind modules. Cannot continue')</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="67" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff">     filters = []</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="69" 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="LC69" class="line" lang="diff">     input_type = fileformat.from_handle(arguments.sequence_file)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff">     output_type = fileformat.from_handle(arguments.output_file)</span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/seqmagick/test/test_subcommands_quality_filter.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/seqmagick/test/test_subcommands_quality_filter.py</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="p">@@ -7,8 +7,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> from seqmagick.subcommands import quality_filter</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" 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="LC76" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from Bio import triefind</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> IS_PYPY = hasattr(sys, 'pypy_version_info')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="p">@@ -194,7 +192,6 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff">                          [i.id for i in actual])</span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-@unittest.skipIf(IS_PYPY, "Bio.trie not available on pypy.")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"> class PrimerBarcodeFilterTestCase(unittest.TestCase):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff">     def setUp(self):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff">         self.sequences = [</span>

</pre>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="p">@@ -240,7 +237,6 @@</span></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff">         self.assertEqual(events, [1, 5])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" 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">

93

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="94" 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="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-@unittest.skipIf(IS_PYPY, "Bio.trie not available on pypy.")</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" 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="LC95" class="line" lang="diff"> class BarcodePrimerTrieTestCase(unittest.TestCase):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" 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="LC96" class="line" lang="diff">     def setUp(self):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" 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="LC97" class="line" lang="diff">         self.barcode_str = """p1d1bc205,TACTAGCG,CATTGCCTATG</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" 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="LC98" class="line" lang="diff"><span class="p">@@ -258,9 +254,9 @@</span></span>

</pre>

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99

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff">         res = quality_filter.parse_barcode_file(self.fp, primer='CATTGCCTATG')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff">         self.assertEqual(9, len(list(res.keys())))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" 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="LC101" class="line" lang="diff">         self.assertEqual('p1d1bc210', res['TACAGTCGCATTGCCTATG'])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" 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="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(None, triefind.match('TACAGTCGCATTGCCTAT', res))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        self.assertEqual(None, quality_filter.trie_match('TACAGTCGCATTGCCTAT', res))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff">         self.assertEqual('TACAGTCGCATTGCCTATG',</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         triefind.match('TACAGTCGCATTGCCTATGCTACCTA', res))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                         quality_filter.trie_match('TACAGTCGCATTGCCTATGCTACCTA', res))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="107" 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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</td>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="108" 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="LC108" class="line" lang="diff">     def test_primer_in_file(self):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" 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">

109

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff">         res = quality_filter.parse_barcode_file(self.fp, primer=None)</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">biopython_1.71_dual_coding_support.patch</span></pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="plaintext">fix-myfunctions-example-file.patch</span>

</pre>

</td>

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3

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<td class="diff-line-num new_line old" data-linenumber="2" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">replace-biopython-trie-with-pygtrie.patch </span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="b3bea44a8f91e14f357ec4e44fced1bde9f0fc6f">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#b3bea44a8f91e14f357ec4e44fced1bde9f0fc6f"><strong>docs/changelog.rst</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

</td>

<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Changes for seqmagick</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">=====================</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">0.8.0</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" 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="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">-----</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4" 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="6" 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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">* Supports Python 3.5+</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">* Drops support for Python 3.4</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">* Fix issue: "seqmagick with no params gives KeyError:None" [GH-77]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">* Fix for Biopython 1.71 dual coding support [GH-76]; also fixes issue: "Translation error with new BioPython" [GH-79]</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" 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">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">* Send logging to stderr, not stdout [GH-75]</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" 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">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num 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">

4

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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">

13

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">0.7.0</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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="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">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">-----</span>

</pre>

</td>

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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="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">

15

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="d0153cac95479af9bfb99b746b633bc8255bb53a">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#d0153cac95479af9bfb99b746b633bc8255bb53a"><strong>docs/index.rst</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" 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="59" 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">@@ -59,10 +59,10 @@ To install the bleeding edge version::</td>

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<td class="diff-line-num old_line" data-linenumber="59" 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">

59

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<td class="diff-line-num new_line" data-linenumber="59" 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">

59

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="60" 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">

60

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<td class="diff-line-num new_line" data-linenumber="60" 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">

60

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">    pip install git+https://github.com/fhcrc/seqmagick.git@master#egg-info=seqmagick</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="61" 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">

61

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<td class="diff-line-num new_line" data-linenumber="61" 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">

61

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="62" 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">

62

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<td class="diff-line-num new_line old" data-linenumber="62" 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">

</td>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">Note that as of version 0.<span class="idiff left right">7.0, this package requires Python 3.4</span>+. If</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="62" 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">

62

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Note that as of version 0.<span class="idiff left right">8.0, this package requires Python 3.5</span>+. If</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" 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">

63

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<td class="diff-line-num new_line" data-linenumber="63" 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">

63

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">you want to use the most recent version compatible with Python 2.7::</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" 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">

64

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<td class="diff-line-num new_line" data-linenumber="64" 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">

64

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" 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">

65

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<td class="diff-line-num new_line old" data-linenumber="65" 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="LC65" class="line" lang="plaintext">  pip install seqmagick==<span class="idiff left right">1</span>.6.2</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="66" 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="65" 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="LC65" class="line" lang="plaintext">  pip install seqmagick==<span class="idiff left right">0</span>.6.2</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" 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">

66

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<td class="diff-line-num new_line" data-linenumber="66" 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">

66

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" 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="67" 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="LC67" class="line" lang="plaintext">Use</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" 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="68" 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="LC68" class="line" lang="plaintext">===</span>

</pre>

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<br>

</li>

<li id="df6ef13e0e421ccbeb52ae3dafc71163e05f4a2b">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#df6ef13e0e421ccbeb52ae3dafc71163e05f4a2b"><strong>examples/apply-function/myfunctions.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,6 @@ def hash_starts_numeric(records):</td>

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<td class="diff-line-num old_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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<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="python"><span class="s" style="color: #d14;">    their sha-1 hash.</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num old_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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<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="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC17" class="line" lang="python">        <span class="n" style="color: #333;">seq_hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">sha1</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)).</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="python">        <span class="n" style="color: #333;">seq_hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">sha1</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">encode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'utf-8'</span></span><span class="p"><span class="idiff right">)</span>).</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_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="LC18" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_hash</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">isdigit</span><span class="p">():</span></span>

</pre>

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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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<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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">record</span></span></pre>

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<br>

</li>

<li id="d5b95025744fd1556a32320b8f795fd339151809">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#d5b95025744fd1556a32320b8f795fd339151809"><strong>requirements-rtd.txt</strong></a>

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1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">biopython</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext">sphinx</span>

</pre>

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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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">pygtrie</span></pre>

</td>

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<br>

</li>

<li id="19359a61ae2446b51b549167b014da2fcf265768">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biopython" rel="nofollow noreferrer noopener" target="_blank">biopython</a>>=1.70</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" 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="2" 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">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pygtrie" rel="nofollow noreferrer noopener" target="_blank">pygtrie</a></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># for development</span>

</pre>

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<td class="diff-line-num 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">

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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">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/wheel" rel="nofollow noreferrer noopener" target="_blank">wheel</a></span>

</pre>

</td>

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<br>

</li>

<li id="91aa5d4c72a3b7266c11a0eec9925cdd76b3b800">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#91aa5d4c72a3b7266c11a0eec9925cdd76b3b800"><strong>seqmagick/subcommands/convert.py</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,8 +6,7 @@ import functools</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Alphabet</span><span class="p">,</span> <span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Alphabet</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IUPAC</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="11" 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="9" 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="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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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="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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqIO</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaIO</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">seqmagick</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">transform</span></span>

</pre>

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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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<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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">seqmagick.fileformat</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">from_handle</span></span>

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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>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,11 +14,11 @@ from seqmagick.fileformat import from_handle</td>

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<td class="diff-line-num 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">

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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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">common</span></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>

</pre>

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17

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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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">ALPHABETS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

</td>

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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

</td>

<td class="diff-line-num new_line old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="python">    <span class="idiff left">    </span><span class="s" style="color: #d14;"><span class="idiff">'dna'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Alphabet</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">generic_dna</span></span><span class="p">,</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">    <span class="idiff left">    </span><span class="s" style="color: #d14;"><span class="idiff">'dna-ambiguous'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IUPAC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ambiguous_dna</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC20" class="line" lang="python">    <span class="idiff left">    </span><span class="s" style="color: #d14;"><span class="idiff">'protein'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Alphabet</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">generic_protein</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="17" 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="LC21" class="line" lang="python">    <span class="idiff left">    </span><span class="s" style="color: #d14;"><span class="idiff">'rna'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Alphabet</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">generic_rna</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC22" class="line" lang="python">    <span class="idiff left">    </span><span class="s" style="color: #d14;"><span class="idiff">'rna-ambiguous'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IUPAC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ambiguous_rna</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">    <span class="s" style="color: #d14;"><span class="idiff left">"dna"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"DNA"</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">    <span class="s" style="color: #d14;"><span class="idiff left">"dna-ambiguous"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"DNA"</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">    <span class="s" style="color: #d14;"><span class="idiff left">"rna"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"RNA"</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">    <span class="s" style="color: #d14;"><span class="idiff left">"rna-ambiguous"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"RNA"</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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="21" 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">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="s" style="color: #d14;"><span class="idiff left">"protein"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"protein"</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line" data-linenumber="23" 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">

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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="24" 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">

24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_options</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="230" 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="229" 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">@@ -230,6 +229,13 @@ def build_parser(parser):</td>

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<td class="diff-line-num new_line" data-linenumber="229" 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="LC229" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="231" 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="230" 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="LC230" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="231" 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="LC231" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="232" 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="LC232" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">append_annotation_iterator</span><span class="p">(</span><span class="n" style="color: #333;">records_iterator</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="p">):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="233" 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="LC234" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records_iterator</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="235" 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="LC235" class="line" lang="python">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"molecule_type"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ALPHABETS</span><span class="p">[</span><span class="n" style="color: #333;">alphabet</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">record</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transform_file</span><span class="p">(</span><span class="n" style="color: #333;">source_file</span><span class="p">,</span> <span class="n" style="color: #333;">destination_file</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Get just the file name, useful for naming the temporary file.</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python">    <span class="n" style="color: #333;">source_file_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">input_format</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">from_handle</span><span class="p">(</span><span class="n" style="color: #333;">source_file</span><span class="p">))</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="249" 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">@@ -249,8 +255,7 @@ def transform_file(source_file, destination_file, arguments):</td>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python">                <span class="n" style="color: #333;">direction</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">directions</span><span class="p">[</span><span class="n" style="color: #333;">direction</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC256" 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="LC257" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Unsorted iterator.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python">        <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">source_file</span><span class="p">,</span> <span class="n" style="color: #333;">source_file_type</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="258" 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="LC253" class="line" lang="python">                <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ALPHABETS</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="258" 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="LC258" class="line" lang="python">        <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">source_file</span><span class="p">,</span> <span class="n" style="color: #333;">source_file_type</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="259" 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="LC259" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="260" 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="LC260" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#########################################</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" 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="320" 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">@@ -315,6 +320,9 @@ def transform_file(source_file, destination_file, arguments):</td>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># loading the entire sequence file up into memory.</span></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Applying transformations, writing to %s"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python">                <span class="n" style="color: #333;">destination_file</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="318" 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="LC323" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Append datatype annotation, mandatory for Nexus files conversion.</span></span>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="325" 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="LC325" class="line" lang="python">            <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">append_annotation_iterator</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python">        <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">,</span> <span class="n" style="color: #333;">destination_file</span><span class="p">,</span> <span class="n" style="color: #333;">destination_file_type</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"></span>

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<br>

</li>

<li id="7aa62f8d9518716248903b7c8bb9a36c457a3b62">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#7aa62f8d9518716248903b7c8bb9a36c457a3b62"><strong>seqmagick/subcommands/primer_trim.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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">@@ -7,8 +7,7 @@ import logging</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">operator</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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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<td class="diff-line-num new_line old" data-linenumber="10" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Alphabet</span><span class="p">,</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">,</span> <span class="n" style="color: #333;">pairwise2</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="10" 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="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Alphabet</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IUPAC</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" 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="10" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">,</span> <span class="n" style="color: #333;">pairwise2</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">seqmagick</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">transform</span><span class="p">,</span> <span class="n" style="color: #333;">fileformat</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" 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="297" 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">@@ -298,8 +297,7 @@ def action(arguments):</td>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">source_file</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python">        <span class="n" style="color: #333;">sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python">            <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">source_file</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python">            <span class="n" style="color: #333;">source_format</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python">            <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">Gapped</span><span class="p">(</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">single_letter_alphabet</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python">            <span class="n" style="color: #333;">source_format</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Locate primers</span></span>

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<td class="diff-line-num old_line" data-linenumber="305" 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="LC303" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">forward_start</span><span class="p">,</span> <span class="n" style="color: #333;">forward_end</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">reverse_start</span><span class="p">,</span> <span class="n" style="color: #333;">reverse_end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locate_primers</span><span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="319" 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="317" 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">@@ -319,8 +317,7 @@ def action(arguments):</td>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python">        <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">source_file</span><span class="p">.</span><span class="n" style="color: #333;">seek</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="LC318" class="line" lang="python">        <span class="n" style="color: #333;">sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python">            <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">source_file</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python">            <span class="n" style="color: #333;">source_format</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python">            <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">Gapped</span><span class="p">(</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">single_letter_alphabet</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python">            <span class="n" style="color: #333;">source_format</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Apply the transformation</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="323" 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="LC323" class="line" lang="python">        <span class="n" style="color: #333;">prune_action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_ACTIONS</span><span class="p">[</span><span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">prune_action</span><span class="p">]</span></span>

</pre>

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<br>

</li>

<li id="6a735fce2f4ff0f1995bdadd69efeeb9f2ac3fc8">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#6a735fce2f4ff0f1995bdadd69efeeb9f2ac3fc8"><strong>seqmagick/subcommands/quality_filter.py</strong></a>

<hr>

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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">@@ -11,16 +11,29 @@ import sys</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>

</pre>

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<td class="diff-line-num old_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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<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="python"></span>

</pre>

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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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<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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

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<td class="diff-line-num old old_line" data-linenumber="14" 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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<td class="diff-line-num new_line old" data-linenumber="14" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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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<td class="diff-line-num new_line old" data-linenumber="14" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">trie</span><span class="p">,</span> <span class="n" style="color: #333;">triefind</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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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<td class="diff-line-num new_line old" data-linenumber="14" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="python">    <span class="n" style="color: #333;">trie</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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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">

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<td class="diff-line-num new_line old" data-linenumber="14" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="python">    <span class="n" style="color: #333;">triefind</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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="14" 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="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pygtrie</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">trie</span></span>

</pre>

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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="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">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqIO</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">QualityIO</span></span>

</pre>

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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="python"></span>

</pre>

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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">

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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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">seqmagick</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fileformat</span><span class="p">,</span> <span class="n" style="color: #333;">__version__</span></span>

</pre>

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<td class="diff-line-num new_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="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">typed_range</span><span class="p">,</span> <span class="n" style="color: #333;">FileType</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="23" 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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="20" 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="LC20" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="21" 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="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">trie_match</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">trie</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="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="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">has_prefix</span><span class="p">(</span><span class="n" style="color: #333;">teststring</span><span class="p">,</span> <span class="n" style="color: #333;">trie</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="23" 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">trie</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="n" style="color: #333;">teststring</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" 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">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" 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">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="29" 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">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">        <span class="n" style="color: #333;">substr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">[:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" 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;">has_prefix</span><span class="p">(</span><span class="n" style="color: #333;">substr</span><span class="p">,</span> <span class="n" style="color: #333;">trie</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="31" 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">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">trie</span><span class="p">.</span><span class="n" style="color: #333;">has_key</span><span class="p">(</span><span class="n" style="color: #333;">substr</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">            <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substr</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" 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">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">longest</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" 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">

35

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line" data-linenumber="37" 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">

37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Default minimummean quality score</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line" data-linenumber="38" 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">

38

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">DEFAULT_MEAN_SCORE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">25.0</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line" data-linenumber="39" 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">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="626" 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="639" 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">@@ -626,7 +639,7 @@ class PrimerBarcodeFilter(BaseFilter):</td>

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<td class="diff-line-num old_line" data-linenumber="626" 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="639" 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="LC639" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">trie</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trie</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="627" 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="640" 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">

640

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="628" 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="641" 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="LC641" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_record</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="629" 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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<td class="diff-line-num new_line old" data-linenumber="642" 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="LC629" class="line" lang="python">        <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trie<span class="idiff left">find</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">trie</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="630" 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="642" 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="LC642" class="line" lang="python">        <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trie<span class="idiff left right">_</span>match</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">trie</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="630" 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">

630

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<td class="diff-line-num new_line" data-linenumber="643" 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">

643

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="631" 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">

631

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<td class="diff-line-num new_line" data-linenumber="644" 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">

644

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">listener</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="632" 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">

632

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<td class="diff-line-num new_line" data-linenumber="645" 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">

645

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<pre style="margin: 0;"> <span id="LC645" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">listener</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="646" 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="659" 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">@@ -646,7 +659,7 @@ def parse_barcode_file(fp, primer=None, header=False):</td>

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<td class="diff-line-num old_line" data-linenumber="646" 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">

646

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<td class="diff-line-num new_line" data-linenumber="659" 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="LC659" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="647" 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="660" 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="LC660" class="line" lang="python"><span class="s" style="color: #d14;">    Any additional columns are ignored</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="648" 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="661" 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">

661

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="649" 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">

649

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<td class="diff-line-num new_line old" data-linenumber="662" 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="LC649" class="line" lang="python">    <span class="n" style="color: #333;">tr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trie</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">t</span>rie</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="650" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="662" 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">

662

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python">    <span class="n" style="color: #333;">tr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trie</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">StringT</span>rie</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="650" 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">

650

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<td class="diff-line-num new_line" data-linenumber="663" 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">

663

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python">    <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">reader</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="651" 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">

651

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<td class="diff-line-num new_line" data-linenumber="664" 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">

664

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="652" 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">

652

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<td class="diff-line-num new_line" data-linenumber="665" 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="LC665" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="680" 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">@@ -680,10 +693,6 @@ def action(arguments):</td>

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"--quality-window-mean-qual specified without "</span></span>

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681

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<td class="diff-line-num new_line" data-linenumber="694" 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">

694

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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python">                         <span class="s" style="color: #d14;">"--quality-window"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python"></span>

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683

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<td class="diff-line-num new_line old" data-linenumber="696" 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="LC683" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">trie</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">triefind</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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684

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<td class="diff-line-num new_line old" data-linenumber="696" 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="LC684" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>

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685

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<td class="diff-line-num new_line old" data-linenumber="696" 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="LC685" class="line" lang="python">            <span class="s" style="color: #d14;">'Missing Bio.trie and/or Bio.triefind modules. Cannot continue'</span><span class="p">)</span></span>

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686

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<pre style="margin: 0;">-<span id="LC686" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="687" 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">

687

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696

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python">    <span class="n" style="color: #333;">filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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688

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<td class="diff-line-num new_line" data-linenumber="697" 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">

697

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python">    <span class="n" style="color: #333;">input_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileformat</span><span class="p">.</span><span class="n" style="color: #333;">from_handle</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">sequence_file</span><span class="p">)</span></span>

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689

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<td class="diff-line-num new_line" data-linenumber="698" 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">

698

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<pre style="margin: 0;"> <span id="LC698" class="line" lang="python">    <span class="n" style="color: #333;">output_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileformat</span><span class="p">.</span><span class="n" style="color: #333;">from_handle</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">output_file</span><span class="p">)</span></span>

</pre>

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</li>

<li id="0650a49d4ac15d63dd5695c48a2badeb9d925786">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#0650a49d4ac15d63dd5695c48a2badeb9d925786"><strong>seqmagick/test/integration/data/input6.fasta</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>test1 test sequence 1 RNA</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AC-GU</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>test2 test sequence 2</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">A-AAA</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">>test3 sequence 3</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">A---A</span></pre>

</td>

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<br>

</li>

<li id="66391cb3b0062ee21bb22d56cf718d57a54d50b0">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#66391cb3b0062ee21bb22d56cf718d57a54d50b0"><strong>seqmagick/test/integration/data/output2.nex</strong></a>

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1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#NEXUS</span>

</pre>

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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">begin data;</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="3" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">       </span>dimensions ntax=3 nchar=5;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="3" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">       </span>format datatype=dna missing=? gap=-;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<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">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">dimensions ntax=3 nchar=5;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">format datatype=dna missing=? gap=-;</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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

</td>

<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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">matrix</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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

</td>

<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">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">test1 AC-GT</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7" 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">

7

</td>

<td class="diff-line-num new_line" data-linenumber="7" 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">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">test2 A-AAA</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8b40d397823d5340dc6f6114c84cd6a1d967026c">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#8b40d397823d5340dc6f6114c84cd6a1d967026c"><strong>seqmagick/test/integration/data/output3.nex</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#NEXUS</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">begin data;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">dimensions ntax=3 nchar=5;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">format datatype=rna missing=? gap=-;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">matrix</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">test1 AC-GU</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">test2 A-AAA</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">test3 A---A</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">end;</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="ef3896f5c1c77ea6efce689d9c056c1c4f28f8c3">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#ef3896f5c1c77ea6efce689d9c056c1c4f28f8c3"><strong>seqmagick/test/integration/data/output4.nex</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#NEXUS</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">begin data;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">dimensions ntax=3 nchar=5;</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

</td>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">format datatype=protein missing=? gap=-;</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">matrix</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">test1 AC-GT</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">test2 A-AAA</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">test3 A---A</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">end;</span></pre>

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<br>

</li>

<li id="82e1c6c9831266d85ede6ec0e472a68670a2054a">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#82e1c6c9831266d85ede6ec0e472a68670a2054a"><strong>seqmagick/test/integration/test_convert.py</strong></a>

<hr>

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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">@@ -97,6 +97,20 @@ class ConvertToNexusTestCase(CommandLineTestMixIn, unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">    <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'convert {input} {output} --output-format nexus --alphabet dna-ambiguous'</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" 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="LC100" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ConvertToNexusRNATestCase</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineTestMixIn</span><span class="p">,</span> <span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python">    <span class="n" style="color: #333;">in_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.fasta'</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python">    <span class="n" style="color: #333;">input_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'input6.fasta'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python">    <span class="n" style="color: #333;">expected_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'output3.nex'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">    <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'convert {input} {output} --output-format nexus --alphabet rna'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" 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="LC106" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" 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="107" 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="LC107" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ConvertToNexusProteinTestCase</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineTestMixIn</span><span class="p">,</span> <span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python">    <span class="n" style="color: #333;">in_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.fasta'</span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python">    <span class="n" style="color: #333;">input_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'input2.fasta'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python">    <span class="n" style="color: #333;">expected_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'output4.nex'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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="LC111" class="line" lang="python">    <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'convert {input} {output} --output-format nexus --alphabet protein'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ConvertUngapCutTestCase</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineTestMixIn</span><span class="p">,</span> <span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">    <span class="n" style="color: #333;">in_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.fasta'</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">    <span class="n" style="color: #333;">out_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.fasta'</span></span>

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<br>

</li>

<li id="f12631b6aa2f26ba5d46a706cbddc73a139cbeb6">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#f12631b6aa2f26ba5d46a706cbddc73a139cbeb6"><strong>seqmagick/test/test_primer_trim.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,6 @@ Tests for primer trim</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</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;">unittest</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></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;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Alphabet</span></span>

</pre>

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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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" 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="69" 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">@@ -70,8 +69,7 @@ class HammingDistanceTestCase(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_alignment_record</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python">        <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">Gapped</span><span class="p">(</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">generic_dna</span><span class="p">)))</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">LocatePrimersTestCase</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

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<br>

</li>

<li id="f52b658e1d9f644a85f4f9e6d945e49f85814b46">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#f52b658e1d9f644a85f4f9e6d945e49f85814b46"><strong>seqmagick/test/test_subcommands_quality_filter.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,8 +7,6 @@ from Bio.SeqRecord import SeqRecord</td>

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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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">seqmagick.subcommands</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">quality_filter</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">triefind</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">IS_PYPY</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">,</span> <span class="s" style="color: #d14;">'pypy_version_info'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" 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="192" 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">@@ -194,7 +192,6 @@ class MaxLengthFilterTestCase(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">                         <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">actual</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">skipIf</span><span class="p">(</span><span class="n" style="color: #333;">IS_PYPY</span><span class="p">,</span> <span class="s" style="color: #d14;">"Bio.trie not available on pypy."</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PrimerBarcodeFilterTestCase</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="240" 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="237" 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">@@ -240,7 +237,6 @@ class RecordEventListenerTestCase(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">events</span><span class="p">,</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">skipIf</span><span class="p">(</span><span class="n" style="color: #333;">IS_PYPY</span><span class="p">,</span> <span class="s" style="color: #d14;">"Bio.trie not available on pypy."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="240" 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="LC240" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BarcodePrimerTrieTestCase</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="246" 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="242" 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="LC242" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">barcode_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""p1d1bc205,TACTAGCG,CATTGCCTATG</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="258" 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="254" 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">@@ -258,9 +254,9 @@ p1d1bc213,TACGAGAC,CAYGGCTA"""</td>

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<td class="diff-line-num old_line" data-linenumber="258" 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="254" 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="LC254" class="line" lang="python">        <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quality_filter</span><span class="p">.</span><span class="n" style="color: #333;">parse_barcode_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'CATTGCCTATG'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="255" 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="LC255" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="260" 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="256" 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="LC256" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="s" style="color: #d14;">'p1d1bc210'</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'TACAGTCGCATTGCCTATG'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="257" 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="LC261" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">triefind</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'TACAGTCGCATTGCCTAT'</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="262" 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="LC257" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">quality_filter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">trie_</span>match</span><span class="p">(</span><span class="s" style="color: #d14;">'TACAGTCGCATTGCCTAT'</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="s" style="color: #d14;">'TACAGTCGCATTGCCTATG'</span><span class="p">,</span></span>

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<td class="diff-line-num new_line old" data-linenumber="259" 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="LC263" class="line" lang="python">                         <span class="n" style="color: #333;"><span class="idiff left">triefind</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'TACAGTCGCATTGCCTATGCTACCTA'</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python">                         <span class="n" style="color: #333;"><span class="idiff left">quality_filter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">trie_</span>match</span><span class="p">(</span><span class="s" style="color: #d14;">'TACAGTCGCATTGCCTATGCTACCTA'</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_primer_in_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">        <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quality_filter</span><span class="p">.</span><span class="n" style="color: #333;">parse_barcode_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">primer</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="00abf6d2722a5596aed9abe31af5e5146fe97133">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#00abf6d2722a5596aed9abe31af5e5146fe97133"><strong>seqmagick/test/test_transform.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,7 +7,7 @@ import functools</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">Alphabet</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="11" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>

</pre>

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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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>

</pre>

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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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<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="python"></span>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,16 +16,13 @@ from seqmagick import transform</td>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">FATAL</span><span class="p">)</span></span>

</pre>

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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="python"></span>

</pre>

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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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<td class="diff-line-num new_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="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_alignment_record</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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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<td class="diff-line-num new_line old" data-linenumber="19" 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="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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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<td class="diff-line-num new_line old" data-linenumber="19" 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="LC20" class="line" lang="python">        <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">Gapped</span><span class="p">(</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">generic_dna</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" 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="19" 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="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">))</span></span>

</pre>

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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">

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<td class="diff-line-num new_line" data-linenumber="20" 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="LC20" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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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<td class="diff-line-num new_line old" data-linenumber="21" 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="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">seqrecord</span><span class="p">(</span><span class="n" style="color: #333;">sequence_id</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_text</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Alphabet</span><span class="p">.</span><span class="n" style="color: #333;">generic_dna</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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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<td class="diff-line-num new_line old" data-linenumber="21" 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="LC23" class="line" lang="python">              <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" 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="21" 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="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">seqrecord</span><span class="p">(</span><span class="n" style="color: #333;">sequence_id</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_text</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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="22" 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="LC22" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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="23" 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="LC23" class="line" lang="python"><span class="s" style="color: #d14;">    Quick shortcut to make a SeqRecord</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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="24" 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="LC24" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="25" 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="LC27" class="line" lang="python">    <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence_text</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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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<td class="diff-line-num new_line old" data-linenumber="25" 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="LC28" class="line" lang="python">                       <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sequence_id</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="29" 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="25" 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="LC25" class="line" lang="python">    <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence_text</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sequence_id</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" 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="26" 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="LC26" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">description</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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="27" 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="LC27" class="line" lang="python">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">description</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">record</span></span>

</pre>

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<br>

</li>

<li id="87b1ac486a071802f654fab8fafaa5df5e186b8b">

<a href="https://salsa.debian.org/med-team/seqmagick/-/compare/c38d7880bb7f05422df40c867aab448ce22ff8cd...304ee0448f44a2eea0867205f97fab1f82dbbe24#87b1ac486a071802f654fab8fafaa5df5e186b8b"><strong>seqmagick/transform.py</strong></a>

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<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 +13,6 @@ import tempfile</td>

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<pre style="margin: 0;"> <span id="LC13" 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="LC14" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Alphabet</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IUPAC</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Data</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CodonTable</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" 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="62" 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">@@ -63,8 +62,7 @@ def dashes_cleanup(records, prune_chars='.:?~'):</td>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">        <span class="s" style="color: #d14;">"Applying _dashes_cleanup: converting any of '{}' to '-'."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prune_chars</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python">    <span class="n" style="color: #333;">translation_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">):</span> <span class="s" style="color: #d14;">'-'</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="n" style="color: #333;">prune_chars</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">translation_table</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python">                         <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">translation_table</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">record</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" 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="167" 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">@@ -169,8 +167,7 @@ def isolate_region(sequences, start, end, gap_char='-'):</td>

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<td class="diff-line-num old_line" data-linenumber="169" 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="LC167" class="line" lang="python">        <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>

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<td class="diff-line-num old_line" data-linenumber="170" 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="LC168" class="line" lang="python">        <span class="n" style="color: #333;">start_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap_char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">start</span></span>

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<td class="diff-line-num old_line" data-linenumber="171" 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="LC169" class="line" lang="python">        <span class="n" style="color: #333;">end_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap_char</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</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;">end</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="170" 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="LC172" class="line" lang="python">        <span class="n" style="color: #333;">seq</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;">start_gap</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;">seq</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="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end_gap</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python">                <span class="n" style="color: #333;">alphabet</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;">alphabet</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="174" 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="170" 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="LC170" class="line" lang="python">        <span class="n" style="color: #333;">seq</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;">start_gap</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;">seq</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="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end_gap</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="171" 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="LC171" class="line" lang="python">        <span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">sequence</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" 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="188" 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">@@ -191,7 +188,7 @@ def drop_columns(records, slices):</td>

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<td class="diff-line-num new_line" data-linenumber="188" 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="LC188" class="line" lang="python">        <span class="n" style="color: #333;">drop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">slice</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">slices</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python">                   <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">slice</span><span class="p">.</span><span class="n" style="color: #333;">indices</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">))))</span></span>

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<td class="diff-line-num new_line" data-linenumber="190" 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="LC190" class="line" lang="python">        <span class="n" style="color: #333;">keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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;">drop</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">))]</span></span>

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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC194" class="line" lang="python">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</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;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">compress</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">keep</span><span class="p">))<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">alphabet</span></span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="195" 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="191" 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="LC191" class="line" lang="python">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</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;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">compress</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">keep</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" 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="192" 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="LC192" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">record</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="196" 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="193" 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="LC193" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="197" 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="194" 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="LC194" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">multi_cut_sequences</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">,</span> <span class="n" style="color: #333;">slices</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="690" 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="687" 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">@@ -690,7 +687,6 @@ def translate(records, translate):</td>

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<td class="diff-line-num old_line" data-linenumber="690" 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">

690

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<td class="diff-line-num new_line" data-linenumber="687" 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="LC687" class="line" lang="python">    <span class="n" style="color: #333;">to_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">translate</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'stop'</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="691" 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="688" 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="LC688" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="692" 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="689" 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="LC689" class="line" lang="python">    <span class="n" style="color: #333;">source_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">translate</span><span class="p">[:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="693" 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">

693

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<td class="diff-line-num new_line old" data-linenumber="690" 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="LC693" class="line" lang="python">    <span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'dna'</span><span class="p">:</span> <span class="n" style="color: #333;">IUPAC</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_dna</span><span class="p">,</span> <span class="s" style="color: #d14;">'rna'</span><span class="p">:</span> <span class="n" style="color: #333;">IUPAC</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_rna</span><span class="p">}[</span><span class="n" style="color: #333;">source_type</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="694" 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="690" 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">

690

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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="695" 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="691" 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="LC691" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Get a translation table</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="696" 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="692" 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="LC692" class="line" lang="python">    <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'dna'</span><span class="p">:</span> <span class="n" style="color: #333;">CodonTable</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_dna_by_name</span><span class="p">[</span><span class="s" style="color: #d14;">"Standard"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="704" 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="700" 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">@@ -704,7 +700,7 @@ def translate(records, translate):</td>

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<td class="diff-line-num old_line" data-linenumber="704" 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">

704

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<td class="diff-line-num new_line" data-linenumber="700" 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">

700

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<pre style="margin: 0;"> <span id="LC700" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="705" 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="701" 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="LC701" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="706" 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="702" 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="LC702" class="line" lang="python">        <span class="n" style="color: #333;">sequence</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;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="707" 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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<td class="diff-line-num new_line old" data-linenumber="703" 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="LC707" class="line" lang="python">        <span class="n" style="color: #333;">seq</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;">sequence</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alphabet</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="708" 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="703" 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="LC703" class="line" lang="python">        <span class="n" style="color: #333;">seq</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;">sequence</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="708" 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">

708

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<td class="diff-line-num new_line" data-linenumber="704" 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">

704

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python">        <span class="n" style="color: #333;">protein</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;">translate</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">to_stop</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">to_stop</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="709" 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">

709

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<td class="diff-line-num new_line" data-linenumber="705" 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">

705

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">protein</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="710" 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">

710

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<td class="diff-line-num new_line" data-linenumber="706" 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">

706

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python"></span>

</pre>

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