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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kleborate">Debian Med / kleborate</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/03f5f01d11be02c4cc36f8c9870fb964118af4b3">03f5f01d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-09T01:14:44+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.1</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3f62198ed5da374a4ef510aa7278cbe9c08cfddc">
kleborate/data/CARD_AMR_clustered.csv
</a>
</li>
<li class="file-stats">
<a href="#a2dea2c3a7f6dc7bf5cccb29aa829392edcb0826">
kleborate/kaptive.py
</a>
</li>
<li class="file-stats">
<a href="#850324ff01a403192c826ab4ad59a2e7912c71d5">
kleborate/version.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="3f62198ed5da374a4ef510aa7278cbe9c08cfddc">
<a href="https://salsa.debian.org/med-team/kleborate/-/commit/03f5f01d11be02c4cc36f8c9870fb964118af4b3#3f62198ed5da374a4ef510aa7278cbe9c08cfddc"><strong>kleborate/data/CARD_AMR_clustered.csv</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1568" style="width: 35px; color: rgba(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="1568" style="width: 35px; color: rgba(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">@@ -1568,8 +1568,7 @@ clusterid,queryID,class,gene,allele,seqID,accession,positions,size,cluster_conta</td>
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<td class="diff-line-num old_line" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1568
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<td class="diff-line-num new_line" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1568
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="plaintext">135,SHV-107,Bla,SHV-OKP-LEN,SHV-107,1568,ARO_3001156,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1569
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<td class="diff-line-num new_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="plaintext">135,SHV-26,Bla,SHV-OKP-LEN,SHV-26,1569,ARO_3001084,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_chr</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1570
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<td class="diff-line-num new_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="plaintext">135,SHV-49,Bla,SHV-OKP-LEN,SHV-49,1570,ARO_3001106,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1571" 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">
1571
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<td class="diff-line-num new_line old" data-linenumber="1571" 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="LC1571" class="line" lang="plaintext">135,SHV-56.v1,Bla,SHV-OKP-LEN,SHV-56.v1,1571,ARG_AY352599,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_ESBL</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1572" 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">
1572
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<td class="diff-line-num new_line old" data-linenumber="1571" 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="LC1572" class="line" lang="plaintext">135,SHV-56.v2,Bla,SHV-OKP-LEN,SHV-56.v2,1572,ARO_3001112,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1573" 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="1571" 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">
1571
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="plaintext">135,SHV-56,Bla,SHV-OKP-LEN,SHV-56,1572,ARO_3001112,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR</span>
</pre>
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1573
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<td class="diff-line-num new_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="plaintext">135,SHV-72,Bla,SHV-OKP-LEN,SHV-72,1573,ARO_3001126,-,-,no,no,inhibitor-resistant class A broad-spectrum beta-lactamase,Bla_inhR</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1574
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<td class="diff-line-num new_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1573
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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="plaintext">135,SHV-110,Bla,SHV-OKP-LEN,SHV-110,1574,ARO_3001159,-,-,no,no,class A extended-spectrum beta-lactamase,Bla_chr</span>
</pre>
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1575
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<td class="diff-line-num new_line" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1574
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="plaintext">135,SHV-145,Bla,SHV-OKP-LEN,SHV-145,1575,ARO_3001185,-,-,no,no,class A extended-spectrum beta-lactamase,Bla_chr</span>
</pre>
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<li id="a2dea2c3a7f6dc7bf5cccb29aa829392edcb0826">
<a href="https://salsa.debian.org/med-team/kleborate/-/commit/03f5f01d11be02c4cc36f8c9870fb964118af4b3#a2dea2c3a7f6dc7bf5cccb29aa829392edcb0826"><strong>kleborate/kaptive.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,7 +70,7 @@ def run_kaptive(kaptive_py, kaptive_db, contigs, output_file, one_thread):</td>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">kaptive_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/kaptive'</span></span>
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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">kaptive_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kaptive_prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_table.txt'</span></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">-<span id="LC73" 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;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'python3</span> '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kaptive_py</span> <span class="o" style="font-weight: 600;">+</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" 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;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">executable</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span> '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kaptive_py</span> <span class="o" style="font-weight: 600;">+</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">' -a '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">contigs</span> <span class="o" style="font-weight: 600;">+</span></span>
</pre>
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75
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">' -k '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kaptive_db</span> <span class="o" style="font-weight: 600;">+</span></span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">' -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kaptive_prefix</span> <span class="o" style="font-weight: 600;">+</span></span>
</pre>
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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">@@ -16,4 +16,4 @@ not, see <http://www.gnu.org/licenses/>.</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" 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;">'2.0.<span class="idiff left right">0</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC19" 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;">'2.0.<span class="idiff left right">1</span>'</span></span></pre>
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