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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/virulencefinder">Debian Med / virulencefinder</a>
</h3>
<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/6840870f7051dbc7997ef05b4a5ff7fdae5bc8f3">6840870f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-06T00:40:24+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.4</pre>
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<h4>1 changed file:</h4>
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<a href="#0b6b00ee57158d0eaebc720f8cc209896b15d878">
virulencefinder.py
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<h4>Changes:</h4>
<li id="0b6b00ee57158d0eaebc720f8cc209896b15d878">
<a href="https://salsa.debian.org/med-team/virulencefinder/-/commit/6840870f7051dbc7997ef05b4a5ff7fdae5bc8f3#0b6b00ee57158d0eaebc720f8cc209896b15d878"><strong>virulencefinder.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="412" 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">@@ -412,6 +412,9 @@ for db in results:</td>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">contig_res</span><span class="p">[</span><span class="n" style="color: #333;">contig_id</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_start"</span><span class="p">],</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_end"</span><span class="p">],</span></span>
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413
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">bit_score</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">])</span></span>
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414
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">contig_res</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"No hit found"</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check for overlapping hits, only report the best</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig_id</span><span class="p">,</span> <span class="n" style="color: #333;">hit_lsts</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_res</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -456,8 +459,8 @@ for db in results:</td>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">function</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write JSON results dict</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="n" style="color: #333;"><span class="idiff left right">header</span></span><span class="p">:</span> <span class="p">{}})</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;"><span class="idiff left right">header</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">].</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="n" style="color: #333;"><span class="idiff left right">contig_id</span></span><span class="p">:</span> <span class="p">{}})</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;"><span class="idiff left right">contig_id</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"> <span class="s" style="color: #d14;">"virulence_gene"</span><span class="p">:</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="s" style="color: #d14;">"identity"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">identity</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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466
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="s" style="color: #d14;">"HSP_length"</span><span class="p">:</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -483,7 +486,7 @@ userinput = {"filename(s)": args.infile,</td>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="s" style="color: #d14;">"method"</span><span class="p">:</span> <span class="n" style="color: #333;">method</span><span class="p">,</span></span>
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="s" style="color: #d14;">"file_format"</span><span class="p">:</span> <span class="n" style="color: #333;">file_format</span><span class="p">}</span></span>
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"><span class="n" style="color: #333;">run_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">date</span><span class="p">,</span> <span class="s" style="color: #d14;">"time"</span><span class="p">:</span> <span class="n" style="color: #333;">time</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"><span class="n" style="color: #333;">json_results</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">json_results</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">lower</span><span class="p">()))</span></span>
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"user_input"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">userinput</span></span>
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"run_info"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_info</span></span>
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"results"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json_results</span></span>
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