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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/virulencefinder">Debian Med / virulencefinder</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/6840870f7051dbc7997ef05b4a5ff7fdae5bc8f3">6840870f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T00:40:24+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/e7ce6ace19bab1e7c355c53d03ba2c169c20ec27">e7ce6ace</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T00:40:25+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.4'
Update to upstream version '2.0.4'
with Debian dir ff87d0246e5bbc989e392cb0831c623ee9a1a847</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/4818e37ea55f1b2d7566de9073c11791668936bb">4818e37e</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T00:43:23+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/u/metadata, Make yamllint happy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/1cc40f8bca76402bf8da491241ab589d709718ff">1cc40f8b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T00:45:39+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump debhelper-compat version to 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/0e9539b9b11a3385f80b0ee2857674bf177c3295">0e9539b9</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T00:45:57+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Declare compliance with policy 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/735aeb69c17a34020be57a01f9347ae6cc0d7203">735aeb69</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-05T19:31:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: dh_installman with language=C
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/257e5e7052f63e968f8b2456a3c6b1996bdf9ac5">257e5e70</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-05T19:38:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/eb5662015d69a3b52387a6e784734850feb9ea6b">eb566201</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T01:19:31+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: Cleanup post testing (makes build reproducible)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/132d78daa72aad8c51a6d03234cd6532c4f30c16">132d78da</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T01:19:31+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<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="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#99cd8b846455369e44dc5019cf32f14422eaa8c0">
<span class="new-file">
+
debian/virulencefinder.py.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b6b00ee57158d0eaebc720f8cc209896b15d878">
virulencefinder.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">virulencefinder (2.0.4-1) UNRELEASED; urgency=medium</span>
</pre>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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"> * Team Upload.</span>
</pre>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version 2.0.4</span>
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<td class="new_line diff-line-num new" 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">
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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"> * Update d/u/metadata, Make yamllint happy</span>
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<td class="new_line diff-line-num new" 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">
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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"> * Bump debhelper-compat version to 13</span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Declare compliance with policy 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * d/rules: dh_installman with language=C</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Add manpages</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * d/rules: Cleanup post testing (makes build reproducible)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Mon, 05 Jul 2021 19:43:45 +0000</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">virulencefinder (2.0.3+git20190809.dde157a-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Team Upload.</span>
</pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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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">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-tabulate,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-cgecore,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> ncbi-blast+ <!nocheck></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/virulencefinder</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/virulencefinder.git</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder</span>
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<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>virulencefinder.py</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export PYBUILD_SYSTEM=custom</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">export PYBUILD_CLEAN_ARGS=rm -rf test/<span class="idiff left right">results_tab.tsv</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">export PYBUILD_CLEAN_ARGS=rm -rf test/<span class="idiff left right">Hit_in_genome_seq.fsa test/Virulence_genes.fsa test/data.json test/tmp test/results_tab.tsv test/results.txt</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,3 +19,6 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> echo "TEST FAILED"; \</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> fi</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_installman --language=C</span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">---</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> - Author: ></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Katrine Grimstrup Joensen and Flemming Scheutz and Ole Lund and Henrik</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,3 +23,6 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Repository: https://bitbucket.org/genomicepidemiology/virulencefinder</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Bug-Database: https://bitbucket.org/genomicepidemiology/virulencefinder/issues</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Bug-Submit: https://bitbucket.org/genomicepidemiology/virulencefinder/issues/new</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Repository-Browse: https://bitbucket.org/genomicepidemiology/virulencefinder</span></pre>
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<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#99cd8b846455369e44dc5019cf32f14422eaa8c0"><strong>debian/virulencefinder.py.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH VIRULENCEFINDER.PY "1" "July 2021" "virulencefinder.py 2.0.4" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">virulencefinder.py \- identify virulence genes in total or partial sequenced isolates of bacteria</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: virulencefinder.py [\-h] \fB\-i\fR INFILE [INFILE ...] [\-o OUTDIR]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[\-tmp TMP_DIR] [\-mp METHOD_PATH] [\-p DB_PATH]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-d DATABASES] [\-l MIN_COV] [\-t THRESHOLD] [\-x]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-speciesinfo_json SPECIESINFO_JSON] [\-q]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-i\fR INFILE [INFILE ...], \fB\-\-infile\fR INFILE [INFILE ...]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">FASTA or FASTQ input files.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-o\fR OUTDIR, \fB\-\-outputPath\fR OUTDIR</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Path to blast output</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-tmp\fR TMP_DIR, \fB\-\-tmp_dir\fR TMP_DIR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Temporary directory for storage of the results from</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">the external software.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-mp\fR METHOD_PATH, \fB\-\-methodPath\fR METHOD_PATH</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Path to method to use (kma or blastn)</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-p\fR DB_PATH, \fB\-\-databasePath\fR DB_PATH</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Path to the databases</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-d\fR DATABASES, \fB\-\-databases\fR DATABASES</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Databases chosen to search in \- if non is specified</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">all is used</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-l\fR MIN_COV, \fB\-\-mincov\fR MIN_COV</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Minimum coverage</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Minimum hreshold for identity</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-x\fR, \fB\-\-extented_output\fR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Give extented output with allignment files, template</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">and query hits in fasta and a tab seperated file with</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">gene profile results</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-\-speciesinfo_json\fR SPECIESINFO_JSON</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Argument used by the cge pipeline. It takes a list in</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">json format consisting of taxonomy, from domain \-></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">species. A database is chosen based on the taxonomy.</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-q\fR, \fB\-\-quiet\fR</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> This manpage was written by Nilesh Patra for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16#0b6b00ee57158d0eaebc720f8cc209896b15d878"><strong>virulencefinder.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -412,6 +412,9 @@ for db in results:</td>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">contig_res</span><span class="p">[</span><span class="n" style="color: #333;">contig_id</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_start"</span><span class="p">],</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_end"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">bit_score</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC415" 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;">contig_res</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"No hit found"</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check for overlapping hits, only report the best</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig_id</span><span class="p">,</span> <span class="n" style="color: #333;">hit_lsts</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_res</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -456,8 +459,8 @@ for db in results:</td>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">function</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write JSON results dict</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="n" style="color: #333;"><span class="idiff left right">header</span></span><span class="p">:</span> <span class="p">{}})</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;"><span class="idiff left right">header</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="n" style="color: #333;"><span class="idiff left right">contig_id</span></span><span class="p">:</span> <span class="p">{}})</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;"><span class="idiff left right">contig_id</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"> <span class="s" style="color: #d14;">"virulence_gene"</span><span class="p">:</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="s" style="color: #d14;">"identity"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">identity</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="s" style="color: #d14;">"HSP_length"</span><span class="p">:</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -483,7 +486,7 @@ userinput = {"filename(s)": args.infile,</td>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="s" style="color: #d14;">"method"</span><span class="p">:</span> <span class="n" style="color: #333;">method</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="s" style="color: #d14;">"file_format"</span><span class="p">:</span> <span class="n" style="color: #333;">file_format</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"><span class="n" style="color: #333;">run_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">date</span><span class="p">,</span> <span class="s" style="color: #d14;">"time"</span><span class="p">:</span> <span class="n" style="color: #333;">time</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"><span class="n" style="color: #333;">json_results</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">json_results</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">lower</span><span class="p">()))</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"user_input"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">userinput</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"run_info"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_info</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"results"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json_results</span></span>
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