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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ariba">Debian Med / ariba</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a">65895acf</a></strong>
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<span>by Sascha Steinbiss</span>
<i>at 2020-09-13T18:30:27+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.14.6+ds</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#31c2a74dc59a82ae4a356c3b011e4bbcdd00c1e1">
ariba/pubmlst_getter.py
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<li class="file-stats">
<a href="#acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4">
ariba/ref_genes_getter.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Change Log</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.14.6](https://github.com/sanger-pathogens/ariba/tree/v2.14.6) (2020-09-07)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.5...v2.14.6</span><span class="p">)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">-</span> PubMLST URL change breaks pubmlstget <span class="p">[</span><span class="nv" style="color: #008080;">\#304</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/304</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> get<span class="se" style="color: #d14;">\_</span>ref card is attempting to download RGI <span class="p">[</span><span class="nv" style="color: #008080;">\#301</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/301</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">-</span> Reference dataset of megares cannot be downloaded <span class="p">[</span><span class="nv" style="color: #008080;">\#287</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/287</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">-</span> Fix for changes in PubMLST url <span class="p">[</span><span class="nv" style="color: #008080;">\#305</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/305</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[rpetit3](https://github.com/rpetit3</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">-</span> Solution 1: for fixing CARD download <span class="p">[</span><span class="nv" style="color: #008080;">\#302</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/302</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[rpetit3](https://github.com/rpetit3</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">-</span> Update CARD citation message <span class="p">[</span><span class="nv" style="color: #008080;">\#289</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/289</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[fmaguire](https://github.com/fmaguire</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.14.5](https://github.com/sanger-pathogens/ariba/tree/v2.14.5) (2020-05-14)</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.4...v2.14.5</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<li id="31c2a74dc59a82ae4a356c3b011e4bbcdd00c1e1">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a#31c2a74dc59a82ae4a356c3b011e4bbcdd00c1e1"><strong>ariba/pubmlst_getter.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,7 +105,7 @@ class PubmlstGetter:</td>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_download_file</span><span class="p">(</span><span class="n" style="color: #333;">profile_url</span><span class="p">,</span> <span class="n" style="color: #333;">profile_outfile</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fasta_url</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_urls</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outdir</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta_url</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'/'</span></span><span class="p"><span class="idiff">)[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">"{0}.tfa"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outdir</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta_url</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'/'</span></span><span class="p"><span class="idiff">)[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_download_file</span><span class="p">(</span><span class="n" style="color: #333;">fasta_url</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tmp'</span><span class="p">)</span></span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">PubmlstGetter</span><span class="p">.</span><span class="n" style="color: #333;">_rename_seqs_in_fasta</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tmp'</span><span class="p">)</span></span>
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<li id="acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a#acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4"><strong>ariba/ref_genes_getter.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,7 +42,7 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_card_versions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Getting available CARD versions'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="p">.</span><span class="n" style="color: #333;">download_file</span><span class="p">(</span><span class="s" style="color: #d14;">'https://card.mcmaster.ca/download'</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="n" style="color: #333;">max_attempts</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">max_download_attempts</span><span class="p">,</span> <span class="n" style="color: #333;">sleep_time</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sleep_time</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'''href="(/download/<span class="idiff left right">0/</span>.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">versions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -183,7 +183,7 @@ class RefGenesGetter:</td>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'You can use them with ARIBA like this:'</span><span class="p">)</span></span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'ariba prepareref -f'</span><span class="p">,</span> <span class="n" style="color: #333;">final_fasta</span><span class="p">,</span> <span class="s" style="color: #d14;">'-m'</span><span class="p">,</span> <span class="n" style="color: #333;">final_tsv</span><span class="p">,</span> <span class="s" style="color: #d14;">'output_directory</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'If you use this downloaded data, please cite:'</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'"<span class="idiff left right">The Comprehensive Antibiotic Resistance Database", McArthur et al 2013, PMID: 23650175</span>'</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'"<span class="idiff left right">CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database", Alcock et al 2020, PMID: 31665441</span>'</span><span class="p">)</span></span>
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187
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'and in your methods say that version'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">'of the database was used'</span><span class="p">)</span></span>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"></span>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -659,6 +659,6 @@ class RefGenesGetter:</td>
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659
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'ariba prepareref -f'</span><span class="p">,</span> <span class="n" style="color: #333;">final_fasta</span><span class="p">,</span> <span class="s" style="color: #d14;">'-m'</span><span class="p">,</span> <span class="n" style="color: #333;">final_tsv</span><span class="p">,</span> <span class="s" style="color: #d14;">'output_directory</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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660
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"></span>
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661
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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662
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">f"Nothing to do. Exiting."</span><span class="p">)</span><span class="idiff left right"> </span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">f"Nothing to do. Exiting."</span><span class="p">)</span></span>
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663
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outprefix</span><span class="p">):</span></span>
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664
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"> <span class="k" style="font-weight: 600;">exec</span><span class="p">(</span><span class="s" style="color: #d14;">'self._get_from_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ref_db</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'(outprefix)'</span><span class="p">)</span></span></pre>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,7 +55,7 @@ vcfcall_mod = Extension(</td>
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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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56
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">minimap_mod</span><span class="p">,</span> <span class="n" style="color: #333;">fermilite_mod</span><span class="p">,</span> <span class="n" style="color: #333;">vcfcall_mod</span><span class="p">],</span></span>
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57
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">,</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.14.<span class="idiff left right">5</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.14.<span class="idiff left right">6</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ARIBA: Antibiotic Resistance Identification By Assembly'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'test_run_data/*'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tb_data/*'</span><span class="p">]},</span></span>
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