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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/scoary">Debian Med / scoary</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/scoary/commit/23fc9602cdf682c3ca1443a1ae4f38d396e2f682">23fc9602</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-29T21:01:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update / create manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scoary/commit/36e0db0f5f9a620838b23d799893862bc8a88317">36e0db0f</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-01-29T21:07:38Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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+
debian/createmanpages
</span>
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</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
debian/manpages
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#3350ee62761a16d386bb97dd13453a6cf54b1eb2">
debian/scoary.1
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<li class="file-stats">
<a href="#27ba55d28d647371e5d1c5dc52d0ba083b764bd4">
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+
debian/vcf2scoary.1
</span>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/scoary/compare/eb831c20be144ae2330ffd844a547d03bf3c88cd...36e0db0f5f9a620838b23d799893862bc8a88317#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">scoary (1.6.16-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">scoary (1.6.16-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">nnnn</span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">920857</span>)</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 29 Jan 2019 <span class="idiff left right">18:26:15</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 29 Jan 2019 <span class="idiff left right">22:07:27</span> +0100</span></pre>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/scoary/compare/eb831c20be144ae2330ffd844a547d03bf3c88cd...36e0db0f5f9a620838b23d799893862bc8a88317#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: teal;">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: navy;">-p</span> <span class="nv" style="color: teal;">$MANDIR</span></span>
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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: teal;">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 $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: teal;">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: navy;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">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: navy;">-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: teal;">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;">This manpage was written by </span><span class="nv" style="color: teal;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>vcf2scoary</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="se" style="color: #d14;">\</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"takes in vcf files and creates a presence/absence matrix of mutations in the Roary/Scoary format"</span> <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" 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: teal;">EOT</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" 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="LC31" 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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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/scoary/compare/eb831c20be144ae2330ffd844a547d03bf3c88cd...36e0db0f5f9a620838b23d799893862bc8a88317#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">scoary</span>.1</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">*</span>.1</span></pre>
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<a href="https://salsa.debian.org/med-team/scoary/compare/eb831c20be144ae2330ffd844a547d03bf3c88cd...36e0db0f5f9a620838b23d799893862bc8a88317#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">@@ -5,3 +5,8 @@ export LC_ALL = C.UTF-8</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh $@ --with python2 --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> echo "Test data are missing so we can not test"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">endif</span></pre>
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<a href="https://salsa.debian.org/med-team/scoary/compare/eb831c20be144ae2330ffd844a547d03bf3c88cd...36e0db0f5f9a620838b23d799893862bc8a88317#3350ee62761a16d386bb97dd13453a6cf54b1eb2"><strong>debian/scoary.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH SCOARY 1 "January 2017"</span>
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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 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SCOARY "1" "January 2019" "scoary 1.6.16" "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="LC3" class="line" lang="plaintext">scoary \- pangenome<span class="idiff left right">\</span>-wide association studies</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">scoary \- pangenome-wide association studies</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">.B scoary</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">.RI [ options ] " files" ...</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">.SH DESCRIPTION</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"><span class="idiff left right">\fBscoary\fP is designed to take the gene_presence_absence.csv file from</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"><span class="idiff left right">.BR roary (1)</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits.</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">It reports a list of genes sorted by strength of association per trait.</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">scoary [\-h] [\-t TRAITS] [\-g GENES] [\-n NEWICKTREE] [\-s START_COL]</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">[\-\-delimiter DELIMITER] [\-r RESTRICT_TO] [\-o OUTDIR] [\-u]</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><span class="idiff left right">[\-p P_VALUE_CUTOFF [P_VALUE_CUTOFF ...]]</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"><span class="idiff left right">[\-c [{I,B,BH,PW,EPW,P} [{I,B,BH,PW,EPW,P} ...]]] [\-m MAX_HITS]</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">[\-\-include_input_columns GRABCOLS] [\-w] [\-\-no\-time] [\-e PERMUTE]</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">[\-\-no_pairwise] [\-\-collapse] [\-\-threads THREADS] [\-\-test]</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><span class="idiff left right">[\-\-citation] [\-\-version]</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">.SH OPTIONS</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">For a complete usage description, see the help menu.</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">.TP</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.B \-h, \-\-help</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Show summary of options.</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">.SH SEE ALSO</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">.BR roary (1)</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">.br</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">/usr/share/doc/scoary/README.md.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.SS "optional arguments:"</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
</pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.SS "Input options:"</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-t\fR TRAITS, \fB\-\-traits\fR TRAITS</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Input trait table (comma\-separated\-values). Trait</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">presence is indicated by 1, trait absence by 0.</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Assumes strain names in the first column and trait</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">names in the first row</span>
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25
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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\-g\fR GENES, \fB\-\-genes\fR GENES</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Input gene presence/absence table (comma\-separatedvalues) from ROARY. Strain names must be equal to</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">those in the trait table</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-n\fR NEWICKTREE, \fB\-\-newicktree\fR NEWICKTREE</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Supply a custom tree (Newick format) for phylogenetic</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">analyses instead instead of calculating it internally.</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-s\fR START_COL, \fB\-\-start_col\fR START_COL</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">On which column in the gene presence/absence file do</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">individual strain info start. Default=15. (1\-based</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">indexing)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-\-delimiter\fR DELIMITER</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">The delimiter between cells in the gene</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">presence/absence and trait files, as well as the</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">output file.</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-r\fR RESTRICT_TO, \fB\-\-restrict_to\fR RESTRICT_TO</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Use if you only want to analyze a subset of your</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">strains. Scoary will read the provided comma\-separated</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">table of strains and restrict analyzes to these.</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.SS "Output options:"</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-o\fR OUTDIR, \fB\-\-outdir\fR OUTDIR</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Directory to place output files. Default = .</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-u\fR, \fB\-\-upgma_tree\fR</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">This flag will cause Scoary to write the calculated</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">UPGMA tree to a newick file</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-p\fR P_VALUE_CUTOFF [P_VALUE_CUTOFF ...], \fB\-\-p_value_cutoff\fR P_VALUE_CUTOFF [P_VALUE_CUTOFF ...]</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">P\-value cut\-off / alpha level. For Fishers,</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Bonferronis, and Benjamini\-Hochbergs tests, SCOARY</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">will not report genes with higher p\-values than this.</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">For empirical p\-values, this is treated as an alpha</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">level instead. I.e. 0.02 will filter all genes except</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">the lower and upper percentile from this test. Run</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">with "\-p 1.0" to report all genes. Accepts standard</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">form (e.g. 1E\-8). Provide a single value (applied to</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">all) or exactly as many values as correction criteria</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">and in corresponding order. (See example under</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">correction). Default = 0.05</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.TP</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">\fB\-c\fR [{I,B,BH,PW,EPW,P} [{I,B,BH,PW,EPW,P} ...]], \fB\-\-correction\fR [{I,B,BH,PW,EPW,P} [{I,B,BH,PW,EPW,P} ...]]</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Apply the indicated filtration measure. Allowed values</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">are I, B, BH, PW, EPW, P. I=Individual (naive)</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">p\-value. B=Bonferroni adjusted p\-value. BH=BenjaminiHochberg adjusted p. PW=Best (lowest) pairwise</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">comparison. EPW=Entire range of pairwise comparison</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">p\-values. P=Empirical p\-value from permutations. You</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">can enter as many correction criteria as you would</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">like. These will be associated with the</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">p_value_cutoffs you enter. For example "\-c I EPW \fB\-p\fR</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">0.1 0.05" will apply the following cutoffs: Naive</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">p\-value must be lower than 0.1 AND the entire range of</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">pairwise comparison values are below 0.05 for this</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">gene. Note that the empirical p\-values should be</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">interpreted at both tails. Therefore, running "\-c P \fB\-p\fR</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">0.05" will apply an alpha of 0.05 to the empirical</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">(permuted) p\-values, i.e. it will filter everything</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">except the upper and lower 2.5 percent of the</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">distribution. Default = Individual p\-value. (I)</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.TP</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">\fB\-m\fR MAX_HITS, \fB\-\-max_hits\fR MAX_HITS</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">Maximum number of hits to report. SCOARY will only</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">report the top max_hits results per trait</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.TP</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">\fB\-\-include_input_columns\fR GRABCOLS</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">Grab columns from the input Roary file. and puts them</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">in the output. Handles comma and ranges, e.g.</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">\fB\-\-include_input_columns\fR 4,6,8,16\-23. The special</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">keyword ALL will include all relevant input columns in</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">the output</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.TP</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-w\fR, \fB\-\-write_reduced\fR</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Use with \fB\-r\fR if you want Scoary to create a new gene</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">presence absence file from your reduced set of</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">isolates. Note: Columns 1\-14 (No. sequences, Avg group</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">size nuc etc) in this file do not reflect the reduced</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">dataset. These are taken from the full dataset.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.TP</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">\fB\-\-no\-time\fR</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">Output file in the form TRAIT.results.csv, instead of</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">TRAIT_TIMESTAMP.csv. When used with the \fB\-w\fR argument</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">will output a reduced gene matrix in the form</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">gene_presence_absence_reduced.csv rather than</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">gene_presence_absence_reduced_TIMESTAMP.csv</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">.SS "Analysis options:"</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">.TP</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">\fB\-e\fR PERMUTE, \fB\-\-permute\fR PERMUTE</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">Perform N number of permutations of the significant</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">results post\-analysis. Each permutation will do a</span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">label switching of the phenotype and a new p\-value is</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">calculated according to this new dataset. After all N</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">permutations are completed, the results are ordered in</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">ascending order, and the percentile of the original</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">result in the permuted p\-value distribution is</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">reported.</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">.TP</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">\fB\-\-no_pairwise\fR</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">Do not perform pairwise comparisons. Inthis mode,</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">Scoary will perform population structure\-naive</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">calculations only. (Fishers test, ORs etc). Useful for</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">summary operations and exploring sets. (Genes unique</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">in groups, intersections etc) but not causal analyses.</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.TP</span>
</pre>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">\fB\-\-collapse\fR</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">Add this to collapse correlated genes (genes that have</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">identical distribution patterns in the sample) into</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">merged units.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.SS "Misc options:"</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">.TP</span>
</pre>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">\fB\-\-threads\fR THREADS</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">Number of threads to use. Default = 1</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">.TP</span>
</pre>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">\fB\-\-test\fR</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">Run Scoary on the test set in exampledata, overriding</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">all other parameters.</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">.TP</span>
</pre>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">\fB\-\-citation\fR</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">Show citation information, and exit.</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">.TP</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">\fB\-\-version\fR</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">Display Scoary version, and exit.</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.PP</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">by Ola Brynildsrud (olbb@fhi.no)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.SH AUTHOR</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="27ba55d28d647371e5d1c5dc52d0ba083b764bd4">
<a href="https://salsa.debian.org/med-team/scoary/compare/eb831c20be144ae2330ffd844a547d03bf3c88cd...36e0db0f5f9a620838b23d799893862bc8a88317#27ba55d28d647371e5d1c5dc52d0ba083b764bd4"><strong>debian/vcf2scoary.1</strong></a>
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1
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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 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH VCF2SCOARY "1" "January 2019" "vcf2scoary 1.6.16" "User Commands"</span>
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3
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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">vcf2scoary \- takes in vcf files and creates a presence/absence matrix of mutations in the Roary/Scoary format</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">vcf2scoary [\-h] [\-\-out OUT] [\-\-types TYPES] [\-\-version] [\-\-force]</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><VCF_file></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><VCF_file></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">The VCF file to convert to Roary/Scoary format</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-\-out\fR OUT</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">The path to the output file</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-\-types\fR TYPES</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">The types of variants to include in the output. NOTE: This</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">works if TYPE=XX can be found in the INFO column of the vcf</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">file. The special keyword ALL includes all types. This is the</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">default setting. Common types are snp, mnp, ins, del and</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">complex. Give as comma\-separated list. Example: \fB\-\-types\fR</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">snp,ins,del</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\-\-version\fR</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">show program's version number and exit</span>
</pre>
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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\-\-force\fR</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Force overwriting of output file. (If it already exists)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.PP</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">by Ola Brynildsrud (olbb@fhi.no)</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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