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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/prokka">Debian Med / prokka</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a">92dfdd23</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-13T11:39:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.14.0+dfsg</pre>
</li>
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<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#f60133a4cdbf56999bb8caf361866b541c61b231">
bin/prokka
</a>
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<li class="file-stats">
<a href="#78e7dafc4ccbbd4e358abb7261b383907fedfcda">
bin/prokka-abricate_to_fasta_db
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<li class="file-stats">
<a href="#8e718194f52500ddc6634eb31abce4134eb40114">
bin/prokka-biocyc_to_fasta_db
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</li>
<li class="file-stats">
<a href="#b139cec3594d68347b4fa9d27e67554372060656">
bin/prokka-cdd_to_hmm
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</li>
<li class="file-stats">
<a href="#5a01ad3f1118cfa710ad84694d00ae4a7e37fcb5">
bin/prokka-clusters_to_hmm
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<li class="file-stats">
<a href="#f1080f4ba32da6679c45e257a22eda7f4cbc877a">
bin/prokka-genbank_to_fasta_db
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<li class="file-stats">
<a href="#e8b90acbf683ddc792cc987b82cf112c214525a6">
bin/prokka-genpept_to_fasta_db
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<li class="file-stats">
<a href="#2877fcdc673a867f46921299db4c1b6cb1b51b00">
bin/prokka-hamap_to_hmm
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<li class="file-stats">
<a href="#d08065d5023ef236e666f9a207456416e9c06d71">
bin/prokka-tigrfams_to_hmm
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<li class="file-stats">
<a href="#2e3063332909bf80733dfec42181ae92c9c79c39">
bin/prokka-uniprot_to_fasta_db
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<li class="file-stats">
<a href="#78371302779ab70a8572cecb42ee0dac246aefef">
test/plasmid.fna
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ brew install brewsci/bio/prokka</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown">If you use <span class="p">[</span><span class="nv" style="color: #008080;">Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://conda.io/docs/install/quick.html</span><span class="p">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown">you can use the <span class="p">[</span><span class="nv" style="color: #008080;">Bioconda channel</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioconda.github.io/</span><span class="p">)</span>:</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">conda install -c conda-forge -c bioconda prokka</span>
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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">conda install -c conda-forge -c bioconda <span class="idiff left right">-c defaults </span>prokka</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Ubuntu/Debian/Mint</span></span>
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<br>
</li>
<li id="f60133a4cdbf56999bb8caf361866b541c61b231">
<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#f60133a4cdbf56999bb8caf361866b541c61b231"><strong>bin/prokka</strong></a>
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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">@@ -19,8 +19,8 @@</td>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">FindBin</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">lib</span> <span class="p">"</span><span class="si" style="color: #d14;">$FindBin</span><span class="s2" style="color: #d14;">::RealBin/../perl5</span><span class="p">";</span> <span class="c1" style="color: #998; font-style: italic;"># for bundled Perl modules</span></span>
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">Cwd</span> <span class="sx" style="color: #d14;">qw(abs_path)</span><span class="p">;</span></span>
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Copy</span><span class="p">;</span></span>
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Time::</span><span class="nv" style="color: #008080;">Piece</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(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">@@ -45,7 +45,7 @@ my @CMDLINE = ($0, @ARGV);</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$OPSYS</span> <span class="o" style="font-weight: 600;">=</span> <span class="vg" style="color: #008080;">$^O</span><span class="p">;</span></span>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$BINDIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$FindBin</span><span class="s2" style="color: #d14;">::RealBin/../binaries/</span><span class="si" style="color: #d14;">$OPSYS</span><span class="p">";</span></span>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$EXE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">FindBin::</span><span class="nv" style="color: #008080;">RealScript</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">1.1<span class="idiff left right">3.7</span></span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">1.1<span class="idiff left right">4.0</span></span><span class="p">";</span></span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">Torsten Seemann <torsten.seemann@gmail.com></span><span class="p">';</span></span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$URL</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">https://github.com/tseemann/prokka</span><span class="p">';</span></span>
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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$PROKKA_PMID</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">24642063</span><span class="p">';</span></span>
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<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#78e7dafc4ccbbd4e358abb7261b383907fedfcda"><strong>bin/prokka-abricate_to_fasta_db</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,7 @@</td>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#>Q92AT0 2.4.1.333~~~~~~1,2-beta-oligoglucan phosphorylase~~~COG3459</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#MTMLKEIKKADLSAAFYPSGELAWLKLKDIMLNQVIQNPLENRLSQIYVRAHVGDKIEIYPLLSRDAEVGFNENGVEYRGVVGPFRYSVQMHFHTRGWFYDVTVDGD</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
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13
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="p">;</span></span>
</pre>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Data::</span><span class="nv" style="color: #008080;">Dumper</span><span class="p">;</span></span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#8e718194f52500ddc6634eb31abce4134eb40114"><strong>bin/prokka-biocyc_to_fasta_db</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="p">;</span></span>
</pre>
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5
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Data::</span><span class="nv" style="color: #008080;">Dumper</span><span class="p">;</span></span>
</pre>
</td>
</tr>
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6
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Text::</span><span class="nv" style="color: #008080;">Unidecode</span> <span class="sx" style="color: #d14;">qw(unidecode)</span><span class="p">;</span></span>
</pre>
</td>
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<br>
</li>
<li id="b139cec3594d68347b4fa9d27e67554372060656">
<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#b139cec3594d68347b4fa9d27e67554372060656"><strong>bin/prokka-cdd_to_hmm</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,7 @@</td>
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2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Data::</span><span class="nv" style="color: #008080;">Dumper</span><span class="p">;</span></span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">AlignIO</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Temp</span> <span class="sx" style="color: #d14;">qw(tempdir)</span><span class="p">;</span></span>
</pre>
</td>
</tr>
</table>
<br>
</li>
<li id="5a01ad3f1118cfa710ad84694d00ae4a7e37fcb5">
<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#5a01ad3f1118cfa710ad84694d00ae4a7e37fcb5"><strong>bin/prokka-clusters_to_hmm</strong></a>
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1
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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Data::</span><span class="nv" style="color: #008080;">Dumper</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Temp</span> <span class="sx" style="color: #d14;">qw(tempdir)</span><span class="p">;</span></span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"></span>
</pre>
</td>
</tr>
</table>
<br>
</li>
<li id="f1080f4ba32da6679c45e257a22eda7f4cbc877a">
<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#f1080f4ba32da6679c45e257a22eda7f4cbc877a"><strong>bin/prokka-genbank_to_fasta_db</strong></a>
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1
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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::Tools::</span><span class="nv" style="color: #008080;">CodonTable</span><span class="p">;</span></span>
</pre>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Data::</span><span class="nv" style="color: #008080;">Dumper</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#e8b90acbf683ddc792cc987b82cf112c214525a6"><strong>bin/prokka-genpept_to_fasta_db</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="p">;</span></span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span><span class="p">(</span><span class="nv" style="color: #008080;">@Options</span><span class="p">,</span> <span class="nv" style="color: #008080;">$verbose</span><span class="p">,</span> <span class="nv" style="color: #008080;">$format</span><span class="p">,</span> <span class="nv" style="color: #008080;">$hypo</span><span class="p">,</span> <span class="nv" style="color: #008080;">$idtag</span><span class="p">,</span> <span class="nv" style="color: #008080;">$sep</span><span class="p">,</span> <span class="nv" style="color: #008080;">$blank</span><span class="p">,</span> <span class="nv" style="color: #008080;">$pseudo</span><span class="p">,</span> <span class="nv" style="color: #008080;">$minlen</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#2877fcdc673a867f46921299db4c1b6cb1b51b00"><strong>bin/prokka-hamap_to_hmm</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="p">;</span></span>
</pre>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Data::</span><span class="nv" style="color: #008080;">Dumper</span><span class="p">;</span></span>
</pre>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Temp</span> <span class="sx" style="color: #d14;">qw(tempdir)</span><span class="p">;</span></span>
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<li id="d08065d5023ef236e666f9a207456416e9c06d71">
<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#d08065d5023ef236e666f9a207456416e9c06d71"><strong>bin/prokka-tigrfams_to_hmm</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">@@ -2,7 +2,7 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="perl"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># These are most/all of the types of lines we need to clean up</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># so that the DESC line has a clean /product we can annotate with</span></span>
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<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#2e3063332909bf80733dfec42181ae92c9c79c39"><strong>bin/prokka-uniprot_to_fasta_db</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">###BREWCONDA###</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">SWISS::</span><span class="nv" style="color: #008080;">Entry</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">SWISS::</span><span class="nv" style="color: #008080;">KW</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#use SWISS::OC;</span></span>
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<a href="https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a#78371302779ab70a8572cecb42ee0dac246aefef"><strong>test/plasmid.fna</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">><span class="idiff left right">gi|383315282|ref|NC_017032.1|</span> Enterococcus faecium Aus0004 plasmid AUS0004_p1, complete sequence</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">><span class="idiff left right">NC_017032.1</span> Enterococcus faecium Aus0004 plasmid AUS0004_p1, complete sequence</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">ATGAATGATTTTAATTATTACAAATCAAAAGAAATTTATCGTGAAAAATATTATCAAATGCCTAAGGTAT</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">TTTTTACTAACGAAAAATACATGGATCTTTCAAATGATGCAAAAATTGCTTATATGCTACTTAAAGATCG</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">ATTTGATTATTCAGTCAAAAATAACTGGGTAGATTCTGATGATAATATATTCTTCATATTCACAGTTGAA</span>
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