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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kaptive">Debian Med / kaptive</a>
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Commits:
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<strong><a href="https://salsa.debian.org/med-team/kaptive/commit/593158b9cc430fd85bf7696628f22cee9184bc26">593158b9</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-01-06T17:17:23+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.7.0</pre>
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<h4>6 changed files:</h4>
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README.md
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extras/Acinetobacter_baumannii_KL_reference_information.pdf
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extras/Acinetobacter_baumannii_OCL_reference_information.pdf
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kaptive.py
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reference_database/Acinetobacter_baumannii_OC_locus_primary_reference.gbk
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reference_database/Acinetobacter_baumannii_k_locus_primary_reference.gbk
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/kaptive/commit/593158b9cc430fd85bf7696628f22cee9184bc26#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">align=</span><span class="s" style="color: #d14;">"center"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"extras/kaptive_logo.png"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Kaptive"</span> <span class="na" style="color: #008080;">width=</span><span class="s" style="color: #d14;">"400"</span><span class="nt" style="color: #000080;">></p></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>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">Kaptive reports information about <span class="idiff left right">K and O types for Klebsiella</span> genome assemblies. You can also run a graphical version of Kaptive via <span class="p">[</span><span class="nv" style="color: #008080;">this web interface</span><span class="p">](</span><span class="sx" style="color: #d14;">http://kaptive.holtlab.net/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[source</span> code](https://github.com/kelwyres/Kaptive-Web)).</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">Kaptive reports information about <span class="idiff left right">surface polysaccharide loci for _Klebsiella_ and _Acinetobacter baumannii_</span> genome assemblies. You can also run a graphical version of Kaptive via <span class="p">[</span><span class="nv" style="color: #008080;">this web interface</span><span class="p">](</span><span class="sx" style="color: #d14;">http://kaptive.holtlab.net/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[source</span> code](https://github.com/kelwyres/Kaptive-Web)).</span>
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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">Given a novel genome and a database of known loci (K<span class="idiff left right"> or O</span>), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">Given a novel genome and a database of known loci (K<span class="idiff left right">, O or OC</span>), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">*</span> BLAST for all known locus nucleotide sequences (using <span class="sb" style="color: #d14;">`blastn`</span>) to identify the best match ('best' defined as having the highest coverage).</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">*</span> Extract the region(s) of the assembly which correspond to the BLAST hits (i.e. the locus sequence in the assembly) and save it to a FASTA file.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">*</span> BLAST for all known locus genes (using <span class="sb" style="color: #d14;">`tblastn`</span>) to identify which expected genes (genes in the best matching locus) are present/missing and whether any unexpected genes (genes from other loci) are present.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">*</span> Output a summary to a table file.</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">In cases where your input assembly closely matches a known locus, Kaptive should make that obvious. When your assembly has a novel type, that too should be clear. However, Kaptive cannot reliably extract or annotate locus sequences for totally novel types – if it indicates a novel locus is present then extracting and annotating the sequence is up to you! Very poor assemblies can confound the results, so be sure to closely examine any case where the locus sequence in your assembly is broken into multiple pieces.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">If you think you have found a novel locus that should be added to one of the databases distributed with Kaptive please <span class="p">[</span><span class="nv" style="color: #008080;">contact us</span><span class="p">](</span><span class="sx" style="color: #d14;">mailto:kaptive.typing@gmail.com</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown">Read more about Kaptive, Kaptive Web and the locus databases in <span class="p">[</span><span class="nv" style="color: #008080;">our papers</span><span class="p">](</span><span class="sx" style="color: #d14;">#citation</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></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">@@ -36,6 +37,7 @@ Read more about Kaptive, Kaptive Web and the locus databases in [our papers](#ci</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Databases distributed with Kaptive</span><span class="p">](</span><span class="sx" style="color: #d14;">#databases-distributed-with-kaptive</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">_Klebsiella_ K locus databases</span><span class="p">](</span><span class="sx" style="color: #d14;">#klebsiella-k-locus-databases</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">_Klebsiella_ O locus database</span><span class="p">](</span><span class="sx" style="color: #d14;">#klebsiella-o-locus-database</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">_Acinetobacter baumannii_ K and OC locus databases</span><span class="p">](</span><span class="sx" style="color: #d14;">#acinetobacter-baumanii-k-and-oc-locus-databases</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">FAQs</span><span class="p">](</span><span class="sx" style="color: #d14;">#faqs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Citation</span><span class="p">](</span><span class="sx" style="color: #d14;">#citation</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">License</span><span class="p">](</span><span class="sx" style="color: #d14;">#license</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" 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="68" 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">@@ -66,7 +68,7 @@ Character codes in the output indicate problems with the locus match:</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown">Kaptive should work on both Python 2 and 3, but <span class="idiff left right">I</span> run/test it on Python 3 and recommend you do the same.</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown">Kaptive should work on both Python 2 and 3, but <span class="idiff left right">we</span> run/test it on Python 3 and recommend you do the same.</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Clone and run</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="281" 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="283" 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">@@ -281,13 +283,15 @@ If you are running this script on a cluster using [SLURM](http://slurm.schedmd.c</td>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Databases distributed with Kaptive</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="markdown">The Kaptive repository contains _Klebsiella_ K-locus and O-locus databases <span class="idiff left">in the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">reference_database</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/katholt/Kaptive/tree/master/reference_database</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> directory, but you can run the</span> Kaptive with any appropriately formatted database of your own.</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="markdown">The Kaptive repository contains _Klebsiella_ K-locus and O-locus databases <span class="idiff left">plus _A. baumannii_ K-locus and OC-locus databases in the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">reference_database</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/katholt/Kaptive/tree/master/reference_database</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> directory, but you can run</span> Kaptive with any appropriately formatted database of your own.</span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="markdown">If you have a locus database that you would like to be added to Kaptive for use by yourself and others in the community, <span class="p">[</span><span class="nv" style="color: #008080;">please get in touch</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/katholt/Kaptive/issues</span><span class="p">)</span>. Similarly, if you have identified new locus variants not currently in the existing databases, let us know!</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="markdown">The databases were developed and curated by <span class="p">[</span><span class="nv" style="color: #008080;">Kelly Wyres</span><span class="p">](</span><span class="sx" style="color: #d14;">https://holtlab.net/kelly-wyres/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">_Klebsiella_</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">Johanna Kenyon</span><span class="p">](</span><span class="sx" style="color: #d14;">https://research.qut.edu.au/infectionandimmunity/projects/bacterial-polysaccharide-research/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">_A.</span> baumannii_).</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="markdown">If you have a locus database that you would like to be added to Kaptive for use by yourself and others in the community, please get in touch via the <span class="p">[</span><span class="nv" style="color: #008080;">issues page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/katholt/Kaptive/issues</span><span class="p">)</span> or <span class="p">[</span><span class="nv" style="color: #008080;">email</span><span class="p">](</span><span class="sx" style="color: #d14;">mailto:kaptive.typing@gmail.com</span><span class="p">)</span> . Similarly, if you have identified new locus variants not currently in the existing databases, let us know!</span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### _Klebsiella_ K locus databases</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="markdown">The primary reference database (<span class="sb" style="color: #d14;">`Klebsiella_k_locus_primary_reference.gbk`</span>) comprises full-length (_galF_ to _ugd_) annotated sequences for each distinct _Klebsiella_ K locus, where available:</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="markdown">The <span class="idiff left right">_Klebsiella_ K locus </span>primary reference database (<span class="sb" style="color: #d14;">`Klebsiella_k_locus_primary_reference.gbk`</span>) comprises full-length (_galF_ to _ugd_) annotated sequences for each distinct _Klebsiella_ K locus, where available:</span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="markdown"><span class="p">*</span> KL1 - KL77 correspond to the loci associated with each of the 77 serologically defined K-type references.</span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="markdown"><span class="p">*</span> KL101 and above are defined from DNA sequence data on the basis of gene content.</span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="markdown"></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">@@ -299,47 +303,65 @@ The variants database (`Klebsiella_k_locus_variant_reference.gbk`) comprises ful</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="markdown"><span class="p">*</span> Deletion variants are named KLN-D1, -D2 etc e.g. KL15-D1 is a deletion variant of KL15.</span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="markdown">Note that KL156-D1 is included in the primary reference database since no full-length version of this locus has been identified to date. </span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="markdown">We recommend screening your data with the primary reference database first to find the best-matching K<span class="idiff left right">-locus type. If you have poor matches or are particularly interested in detecting variant loci you should try the variant database.</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="markdown">We recommend screening your data with the primary reference database first to find the best-matching K<span class="idiff left right"> locus type. If you have poor matches or are particularly interested in detecting variant loci you should try the variant database. </span></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="markdown">WARNING: If you use the variant database please inspect your results carefully and decide for yourself what constitutes a confident match! Kaptive is not optimised for accurate variant detection. </span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="markdown">Database versions:</span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="markdown"><span class="p">*</span> Kaptive releases v0.5.1 and below include the original K locus databases, as described in <span class="p">[</span><span class="nv" style="color: #008080;">Wyres, K. et al. Microbial Genomics (2016).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000102</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.6.0 includes four novel primary <span class="idiff left right">reference loci defined on the basis of gene content: KL162-KL165</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="markdown"><span class="p">*</span> Kaptive releases v0.5.1 and below include the original <span class="idiff left right">_Klebsiella_ </span>K locus databases, as described in <span class="p">[</span><span class="nv" style="color: #008080;">Wyres, K. et al. Microbial Genomics (2016).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000102</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.6.0 includes four novel primary <span class="idiff left">_Klebsiella_ K locus references defined on the basis of gene content (KL162-KL165) in this </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">paper.</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://www.biorxiv.org/content/10.1101/557785v1</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### _Klebsiella_ O locus database</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="markdown">The O locus database (<span class="sb" style="color: #d14;">`Klebsiella_o_locus_primary_reference.gbk`</span>) contains annotated sequences for 12 distinct _Klebsiella_ O loci.</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="markdown">The <span class="idiff left right">_Klebsiella_ </span>O locus database (<span class="sb" style="color: #d14;">`Klebsiella_o_locus_primary_reference.gbk`</span>) contains annotated sequences for 12 distinct _Klebsiella_ O loci.</span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="markdown">O locus classification requires some special logic, as the O1 and O2 serotypes contain the same locus genes. It is two additional genes elsewhere in the chromosome (_wbbY_ and _wbbZ_) which results in the O1 antigen. Kaptive therefore looks for these genes to properly call an assembly as either O1 or O2. When only one of the two additional genes can be found, the result is ambiguous and Kaptive will report a locus type of O1/O2.</span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="markdown">Read more about the O locus and its classification here: <span class="p">[</span><span class="nv" style="color: #008080;">The diversity of _Klebsiella_ pneumoniae surface polysaccharides</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320592/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown">Database versions:</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.4.0 and above include the original version of the _Klebsiella_ O locus database, as described in <span class="p">[</span><span class="nv" style="color: #008080;">Wick, R. et al. J Clin Microbiol (2019).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://jcm.asm.org/content/56/6/e00197-18</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### _Acinetobacter baunannii_ K and OC locus databases</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="markdown">The _A. baumannii_ K (capsule) locus reference database (<span class="sb" style="color: #d14;">`Acinetobacter_baumannii_k_locus_primary_reference.gbk`</span>) contains annotated sequences for 92 distinct K loci.</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="markdown">The _A. baumannii_ OC (lipooligosaccharide outer core) locus reference database (<span class="sb" style="color: #d14;">`Acinetobacter_baumannii_OC_locus_primary_reference.gbk`</span>) contains annotated sequences for 12 distinct OC loci.</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="markdown">WARNING: These databases have been developed and tested specifically for _A. baumannii_ and may not be suitable for screening other _Acinetobacter_ species. You can check that your assembly is a true _A. baumannii_ by screening for the _oxaAB_ gene e.g. using blastn.</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="markdown"> Database versions:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.7.0 and above include the original _A. baumannii_ K and OC locus databases, as described in Wyres, KL. et al. _In prep_ 2019.</span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## FAQs</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Why are there <span class="idiff left right">K-locus genes found outside the K-</span>locus?</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Why are there <span class="idiff left right">locus genes found outside the </span>locus?</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="markdown"><span class="idiff left right">A</span> number of the K-locus genes are orthologous to genes outside of the K-locus region of the genome. E.g the _Klebsiella_ K-locus <span class="nt" style="color: #000080;"><i></span>man<span class="nt" style="color: #000080;"></i></span> and <span class="nt" style="color: #000080;"><i></span>rml<span class="nt" style="color: #000080;"></i></span> genes have orthologues in the LPS (lipopolysacharide) locus; so it is not unusual to find a small number of genes "outside" the locus.</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="markdown"><span class="idiff left right">For _Klebsiella_ K loci in particular, a</span> number of the K-locus genes are orthologous to genes outside of the K-locus region of the genome. E.g the _Klebsiella_ K-locus <span class="nt" style="color: #000080;"><i></span>man<span class="nt" style="color: #000080;"></i></span> and <span class="nt" style="color: #000080;"><i></span>rml<span class="nt" style="color: #000080;"></i></span> genes have orthologues in the LPS (lipopolysacharide) locus; so it is not unusual to find a small number of genes "outside" the locus.</span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="markdown">However, if you have a large number of genes (>5) outside the locus it may mean that there is a problem with the locus match, or that your assembly is very fragmented or contaminated (contains more than one sample).</span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### How can my sample be missing <span class="idiff left right">K-locus genes when it has a full-length, high identity K-</span>locus match?</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### How can my sample be missing <span class="idiff left right">locus genes when it has a full-length, high identity </span>locus match?</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="markdown">Kaptive uses 'tblastn' to screen for the presence of each <span class="idiff left right">K-</span>locus gene with a coverage threshold of 90%. A single non-sense mutation or small indel in the centre of a gene will interrupt the 'tblastn' match and cause it to fall below the 90% threshold. However, such a small change has only a minor effect on the nucleotide 'blast' match across the full locus.</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="markdown">Kaptive uses 'tblastn' to screen for the presence of each locus gene with a coverage threshold of 90%. A single non-sense mutation or small indel in the centre of a gene will interrupt the 'tblastn' match and cause it to fall below the 90% threshold. However, such a small change has only a minor effect on the nucleotide 'blast' match across the full locus.</span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Why does the K-locus region of my sample contain a <i>ugd</i> gene matching another locus?</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Why does the <span class="idiff left right">_Klebsiella_ </span>K-locus region of my sample contain a <i>ugd</i> gene matching another locus?</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="markdown">A small number of the original <span class="idiff left right">K-</span>locus references are truncated, containing only a partial <span class="nt" style="color: #000080;"><i></span>ugd<span class="nt" style="color: #000080;"></i></span> sequence. The reference annotations for these loci do not include <span class="nt" style="color: #000080;"><i></span>ugd<span class="nt" style="color: #000080;"></i></span>, so are not identified by the 'tblastn' search. Instead <span class="nt" style="color: #000080;"><b></span>Kaptive<span class="nt" style="color: #000080;"></b></span> reports the closest match to the partial sequence (if it exceeds the 90% coverage threshold). </span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown">A small number of the original <span class="idiff left right">_Klebsiella_ K </span>locus references are truncated, containing only a partial <span class="nt" style="color: #000080;"><i></span>ugd<span class="nt" style="color: #000080;"></i></span> sequence. The reference annotations for these loci do not include <span class="nt" style="color: #000080;"><i></span>ugd<span class="nt" style="color: #000080;"></i></span>, so are not identified by the 'tblastn' search. Instead <span class="nt" style="color: #000080;"><b></span>Kaptive<span class="nt" style="color: #000080;"></b></span> reports the closest match to the partial sequence (if it exceeds the 90% coverage threshold). </span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="markdown">If you use Kaptive and/or the K locus database in your research, please cite this paper:</span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;"><span class="idiff left right">Wyres, K. et al. </span>Identification of _Klebsiella_ capsule synthesis loci from whole genome data. Microbial Genomics (2016).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000102</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="markdown">If you use Kaptive and/or the <span class="idiff left right">_Klebsiella_ </span>K locus database in your research, please cite this paper:</span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Identification of _Klebsiella_ capsule synthesis loci from whole genome data. Microbial Genomics (2016).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000102</span><span class="p">)</span></span>
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339
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="markdown">If you use <span class="p">[</span><span class="nv" style="color: #008080;">Kaptive Web</span><span class="p">](</span><span class="sx" style="color: #d14;">http://kaptive.holtlab.net/</span><span class="p">)</span> and/or the O locus database in your research, please cite this paper:</span>
</pre>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="markdown">If you use <span class="p">[</span><span class="nv" style="color: #008080;">Kaptive Web</span><span class="p">](</span><span class="sx" style="color: #d14;">http://kaptive.holtlab.net/</span><span class="p">)</span> and/or the <span class="idiff left right">_Klebsiella_ </span>O locus database in your research, please cite this paper:</span>
</pre>
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341
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for _Klebsiella_ genomes. Journal of Clinical Microbiology (2018).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://jcm.asm.org/content/56/6/e00197-18</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="markdown">If you use the _A. baumannii_ K or OC locus database(s) in your research please cite this paper:</span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="markdown">Identification of _Acinetobacter baumannii_ loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Wyres KL, Cahill SM, Holt KE, Hall RM and Kenyon JJ. _In preparation_. </span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="markdown">Lists of papers describing each of the individual _A. baumannii_ reference loci can be found <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/katholt/Kaptive/tree/master/extras</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>
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<a href="https://salsa.debian.org/med-team/kaptive/commit/593158b9cc430fd85bf7696628f22cee9184bc26#cf2ba678e8c048b037edb9ab0a61e424867702c6"><strong>extras/Acinetobacter_baumannii_KL_reference_information.pdf</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">@@ -488,6 +488,17 @@ def protein_blast(assembly, k_locus, gene_seqs, args):</td>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_blast_hits</span><span class="p">(</span><span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">gene_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">genes</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="LC490" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hits</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_cov</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_gene_cov</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pident</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_gene_id</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">best_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">expected_gene</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">k_locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_names</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">best_hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_best_hit_for_query</span><span class="p">(</span><span class="n" style="color: #333;">hits</span><span class="p">,</span> <span class="n" style="color: #333;">expected_gene</span><span class="p">,</span> <span class="n" style="color: #333;">k_locus</span><span class="p">)</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">best_hit</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">best_hits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">best_hit</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">best_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">best_hits</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bitscore</span><span class="p">,</span> <span class="n" style="color: #333;">reverse</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="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">best_hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">best_hits</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">best_hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hits</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cull_conflicting_hits</span><span class="p">(</span><span class="n" style="color: #333;">best_hit</span><span class="p">,</span> <span class="n" style="color: #333;">hits</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"> <span class="n" style="color: #333;">expected_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">expected_gene</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">k_locus</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_names</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">best_hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_best_hit_for_query</span><span class="p">(</span><span class="n" style="color: #333;">hits</span><span class="p">,</span> <span class="n" style="color: #333;">expected_gene</span><span class="p">,</span> <span class="n" style="color: #333;">k_locus</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">@@ -1774,11 +1785,12 @@ def makeblastdb(fasta):</td>
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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="python"><span class="s" style="color: #d14;"> If the FASTA file is not compressed, this just runs makeblastdb. If it is compressed,</span></span>
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1786
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<pre style="margin: 0;"> <span id="LC1786" class="line" lang="python"><span class="s" style="color: #d14;"> it runs gunzip and pipes into makeblastdb.</span></span>
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1776
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1787
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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1788
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<pre style="margin: 0;">+<span id="LC1788" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">' '</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1777" 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="1789" 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">
1789
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<pre style="margin: 0;">+<span id="LC1789" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'WARNING: spaces in file paths may not work in BLAST'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1777" 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">
1777
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<td class="diff-line-num new_line" data-linenumber="1790" 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">
1790
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<pre style="margin: 0;"> <span id="LC1790" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">get_compression_type</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'gz'</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="1778" 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">
1778
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<td class="diff-line-num new_line" data-linenumber="1791" 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">
1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="python"> <span class="n" style="color: #333;">gunzip_command</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'gunzip'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-c'</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</span><span class="p">]</span></span>
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<td class="diff-line-num old_line" data-linenumber="1779" 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">
1779
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<td class="diff-line-num new_line" data-linenumber="1792" 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">
1792
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<pre style="margin: 0;"> <span id="LC1792" class="line" lang="python"> <span class="n" style="color: #333;">makeblastdb_command</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'makeblastdb'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-dbtype'</span><span class="p">,</span> <span class="s" style="color: #d14;">'nucl'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-in'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-out'</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1780" 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">
1780
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<td class="diff-line-num new_line" data-linenumber="1793" 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">
1793
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<pre style="margin: 0;"> <span id="LC1793" class="line" lang="python"> <span class="s" style="color: #d14;">'-title'</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1781" 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">
1781
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<td class="diff-line-num new_line old" data-linenumber="1794" 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="LC1781" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="1782" 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">
1782
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<td class="diff-line-num new_line" data-linenumber="1794" 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">
1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="python"> <span class="n" style="color: #333;">gunzip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">gunzip_command</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1783" 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">
1783
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<td class="diff-line-num new_line" data-linenumber="1795" 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">
1795
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<pre style="margin: 0;"> <span id="LC1795" class="line" lang="python"> <span class="n" style="color: #333;">makeblastdb_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">makeblastdb_command</span><span class="p">,</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gunzip</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1784" 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">
1784
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<td class="diff-line-num new_line" data-linenumber="1796" 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">
1796
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<pre style="margin: 0;"> <span id="LC1796" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>
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