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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/parsnp">Debian Med / parsnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/commit/39bab4561e3395ce3315c468c2d6c09e2830b1fa">39bab456</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-14T10:17:05Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.1+dfsg</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
</a>
</li>
<li class="file-stats">
<a href="#50e9f8fb17151457a31901c72f33d2bcafa9e1a1">
Parsnp.py
</a>
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<li class="file-stats">
<a href="#84bc0ed2d88b3c731434e92eda347d97bd9d28cf">
build_parsnp_linux.sh
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<li class="file-stats">
<a href="#7aed50886f48c76682f73aa91239f317031d0670">
build_parsnp_osx.sh
</a>
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<li class="file-stats">
<a href="#f70362ee3b338a3c3a0b866ec092e0439c9d019c">
install.py
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<li class="file-stats">
<a href="#2e8ce15c0b817fa44897094ab9c5f2c504a96ccd">
script/shuffle.py
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<h4>Changes:</h4>
<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">
<a href="https://salsa.debian.org/med-team/parsnp/commit/39bab4561e3395ce3315c468c2d6c09e2830b1fa#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Copyright (c) 2014, MarBL</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">All rights reserved.</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">PURPOSE</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Parsnp is a command-line-tool for efficient microbial core genome alignment </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">and SNP detection. Parsnp was designed to work in tandem with Gingr, </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">a flexible platform for visualizing genome alignments and phylogenetic trees; </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">both Parsnp and Gingr form part of the Harvest suite. Parsnp is implemented in C++ and Python.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">COPYRIGHT LICENSE</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Copyright © 2014, Battelle National Biodefense Institute (BNBI);</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">all rights reserved. Authored by: Brian Ondov, Todd Treangen, and</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Adam Phillippy</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">This Software was prepared for the Department of Homeland Security</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">(DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">part of contract HSHQDC-07-C-00020 to manage and operate the National</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Biodefense Analysis and Countermeasures Center (NBACC), a Federally</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Funded Research and Development Center.</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Redistribution and use in source and binary forms, with or without</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">modification, are permitted provided that the following conditions are met:</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">* Redistributions of source code must retain the above copyright notice, this</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">* Redistributions in binary form must reproduce the above copyright notice,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> this list of conditions and the following disclaimer in the documentation</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> and/or other materials provided with the distribution.</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">* Neither the name of the {organization} nor the names of its</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> contributors may be used to endorse or promote products derived from</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> this software without specific prior written permission.</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></pre>
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<td class="old_line diff-line-num" 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>
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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">\ No newline at end of file</td>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">modification, are permitted provided that the following conditions are</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">met:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">1. Redistributions of source code must retain the above copyright</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">notice, this list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">2. Redistributions in binary form must reproduce the above copyright</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">notice, this list of conditions and the following disclaimer in the</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">3. Neither the name of the copyright holder nor the names of its</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">contributors may be used to endorse or promote products derived from</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">this software without specific prior written permission.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/commit/39bab4561e3395ce3315c468c2d6c09e2830b1fa#50e9f8fb17151457a31901c72f33d2bcafa9e1a1"><strong>Parsnp.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,7 +93,7 @@ else:</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handler</span><span class="p">(</span><span class="n" style="color: #333;">signum</span><span class="p">,</span> <span class="n" style="color: #333;">frame</span><span class="p">):</span></span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">SIGINT</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">SIGINT</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">'Caught request to terminate by user (CTRL+C), exiting now, bye'</span></span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Caught request to terminate by user (CTRL+C), exiting now, bye'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">128</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SIGINT</span><span class="p">,</span> <span class="n" style="color: #333;">handler</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">@@ -231,66 +231,66 @@ if os.path.exists("%s/MUMmer/nucmer_run"%(PARSNP_DIR)):</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">version</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">VERSION</span></span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">VERSION</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">usage</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"usage: parsnp [options] [-g|-r|-q](see below) -d <genome_dir> -p <threads>"</span></span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"Parsnp quick start for three example scenarios: "</span></span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"1) With reference & genbank file: "</span></span></span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" >parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d <genome_dir> -p <threads> "</span></span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
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243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"2) With reference but without genbank file:"</span></span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" >parsnp -r <reference_genome> -d <genome_dir> -p <threads> "</span></span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"3) Autorecruit reference to a draft assembly:"</span></span></span>
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247
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" >parsnp -q <draft_assembly> -d <genome_db> -p <threads> "</span></span></span>
</pre>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
</pre>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"[Input parameters]"</span></span></span>
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250
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<<input/output>>"</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="251" 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">
251
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -c = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)"</span></span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="252" 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">
252
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -d = <path>: (d)irectory containing genomes/contigs/scaffolds"</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="253" 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">
253
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -r = <path>: (r)eference genome (set to ! to pick random one from genome dir)"</span></span></span>
</pre>
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254
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -g = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None)"</span></span></span>
</pre>
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255
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -o = <string>: output directory? default [./P_CURRDATE_CURRTIME]"</span></span></span>
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256
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)"</span></span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
</pre>
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258
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<<MUMi>>"</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="259" 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">
259
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -U = <float>: max MUMi distance value for MUMi distribution "</span></span></span>
</pre>
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260
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<td class="diff-line-num new_line old" data-linenumber="237" 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="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -M = <flag>: calculate MUMi and exit? overrides all other choices! (default: NO)"</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="237" 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">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"usage: parsnp [options] [-g|-r|-q](see below) -d <genome_dir> -p <threads>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="238" 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">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="261" 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="239" 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">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Parsnp quick start for three example scenarios: "</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="240" 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">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"1) With reference & genbank file: "</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" >parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d <genome_dir> -p <threads> "</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="242" 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">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"2) With reference but without genbank file:"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="244" 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">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" >parsnp -r <reference_genome> -d <genome_dir> -p <threads> "</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"3) Autorecruit reference to a draft assembly:"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" >parsnp -q <draft_assembly> -d <genome_db> -p <threads> "</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="249" 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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"[Input parameters]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"<<input/output>>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -c = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -d = <path>: (d)irectory containing genomes/contigs/scaffolds"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -r = <path>: (r)eference genome (set to ! to pick random one from genome dir)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -g = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -o = <string>: output directory? default [./P_CURRDATE_CURRTIME]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="261" 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="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"<<MUMi>>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -U = <float>: max MUMi distance value for MUMi distribution "</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -M = <flag>: calculate MUMi and exit? overrides all other choices! (default: NO)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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261
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<td class="diff-line-num new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new, mutually exclusive</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="262" 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">
262
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<td class="diff-line-num new_line old" data-linenumber="262" 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="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -i = <float>: max MUM(i) distance (default: autocutoff based on distribution of MUMi values)"</span></span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="263" 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">
263
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<td class="diff-line-num new_line old" data-linenumber="262" 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="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="idiff right"> </span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<<MUM search>>"</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="265" 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="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -i = <float>: max MUM(i) distance (default: autocutoff based on distribution of MUMi values)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"<<MUM search>>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new, default to lower, 12-17</span></span>
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266
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -a = <int>: min (a)NCHOR length (default = 1.1*Log(S))"</span></span></span>
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267
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -C = <int>: maximal cluster D value? (default=100)"</span></span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -z = <path>: min LCB si(z)e? (default = 25)"</span></span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
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270
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<<LCB alignment>>"</span></span></span>
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271
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -D = <float>: maximal diagonal difference? Either percentage (e.g. 0.2) or bp (e.g. 100bp) (default = 0.12)"</span></span> </span>
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272
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -e = <flag> greedily extend LCBs? experimental! (default = NO)"</span></span></span>
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273
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -n = <string>: alignment program (default: libMUSCLE)"</span></span> </span>
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<td class="diff-line-num old old_line" data-linenumber="274" 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">
274
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -u = <flag>: output unaligned regions? .unaligned (default: NO)"</span></span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
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276
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<td class="diff-line-num new_line old" data-linenumber="266" 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="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<<Recombination filtration>>"</span></span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -a = <int>: min (a)NCHOR length (default = 1.1*Log(S))"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -C = <int>: maximal cluster D value? (default=100)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -z = <path>: min LCB si(z)e? (default = 25)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"<<LCB alignment>>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -D = <float>: maximal diagonal difference? Either percentage (e.g. 0.2) or bp (e.g. 100bp) (default = 0.12)"</span></span><span class="p"><span class="idiff right">)</span></span> </span>
</pre>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -e = <flag> greedily extend LCBs? experimental! (default = NO)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -n = <string>: alignment program (default: libMUSCLE)"</span></span><span class="p"><span class="idiff right">)</span></span> </span>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -u = <flag>: output unaligned regions? .unaligned (default: NO)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"<<Recombination filtration>>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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277
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new, default is OFF</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -x = <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO)"</span></span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
</pre>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<<Misc>>"</span></span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -h = <flag>: (h)elp: print this message and exit"</span></span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -p = <int>: number of threads to use? (default= 1)"</span></span></span>
</pre>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -P = <int>: max partition size? limits memory usage (default= 15000000)"</span></span></span>
</pre>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -v = <flag>: (v)erbose output? (default = NO)"</span></span></span>
</pre>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">" -V = <flag>: output (V)ersion and exit"</span></span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -x = <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"<<Misc>>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -h = <flag>: (h)elp: print this message and exit"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -p = <int>: number of threads to use? (default= 1)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -P = <int>: max partition size? limits memory usage (default= 15000000)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -v = <flag>: (v)erbose output? (default = NO)"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" -V = <flag>: output (V)ersion and exit"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#hidden, not yet supported options</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"-q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)"</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"-s = <flag>: (s)plit genomes by n's (default = NO)"</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"-z = <path>: min cluster si(z)e? (default = 10)"</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"-F = <flag>: fast MUMi calc? (default=NO)"</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"-g = <bool>: auto-launch (g)ingr? (default = NO)"</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"-q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)"</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"-s = <flag>: (s)plit genomes by n's (default = NO)"</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"-z = <path>: min cluster si(z)e? (default = 10)"</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"-F = <flag>: fast MUMi calc? (default=NO)"</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"-g = <bool>: auto-launch (g)ingr? (default = NO)"</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="301" 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>
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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">@@ -301,9 +301,9 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">opts</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;">getopt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:],</span> <span class="s" style="color: #d14;">"hxved:C:F:D:i:g:m:MU:o:a:cln:p:P:q:r:Rsz:uV"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span><span class="s" style="color: #d14;">"xtrafast"</span><span class="p">,</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span><span class="s" style="color: #d14;">"extend"</span><span class="p">,</span><span class="s" style="color: #d14;">"sequencedir"</span><span class="p">,</span><span class="s" style="color: #d14;">"clusterD"</span><span class="p">,</span><span class="s" style="color: #d14;">"DiagonalDiff"</span><span class="p">,</span><span class="s" style="color: #d14;">"iniFile"</span><span class="p">,</span><span class="s" style="color: #d14;">"genbank"</span><span class="p">,</span><span class="s" style="color: #d14;">"mumlength"</span><span class="p">,</span><span class="s" style="color: #d14;">"onlymumi"</span><span class="p">,</span><span class="s" style="color: #d14;">"MUMi"</span><span class="p">,</span><span class="s" style="color: #d14;">"outputDir"</span><span class="p">,</span><span class="s" style="color: #d14;">"anchorlength"</span><span class="p">,</span><span class="s" style="color: #d14;">"curated"</span><span class="p">,</span><span class="s" style="color: #d14;">"layout"</span><span class="p">,</span><span class="s" style="color: #d14;">"aligNmentprog"</span><span class="p">,</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span><span class="s" style="color: #d14;">"max-partition-size"</span><span class="p">,</span><span class="s" style="color: #d14;">"query"</span><span class="p">,</span><span class="s" style="color: #d14;">"reference"</span><span class="p">,</span><span class="s" style="color: #d14;">"nofiltreps"</span><span class="p">,</span><span class="s" style="color: #d14;">"split"</span><span class="p">,</span><span class="s" style="color: #d14;">"minclustersiZe"</span><span class="p">,</span><span class="s" style="color: #d14;">"unaligned"</span><span class="p">,</span><span class="s" style="color: #d14;">"version"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">getopt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetoptError</span><span class="p"><span class="idiff left right">,</span></span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">getopt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetoptError</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print help information and exit: </span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">err</span></span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">err</span></span><span class="p"><span class="idiff right">)</span>)</span> </span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">usage</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="359" 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="359" 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">@@ -359,7 +359,7 @@ if __name__ == "__main__":</td>
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359
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">usage</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"-R"</span><span class="p">,</span><span class="s" style="color: #d14;">"--filtreps"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"WARNING: -R option is no longer supported, ignoring. Please see harvest.readthedocs.org for bed filtering w/ harvesttools"</span></span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"WARNING: -R option is no longer supported, ignoring. Please see harvest.readthedocs.org for bed filtering w/ harvesttools"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">filtreps</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"-r"</span><span class="p">,</span><span class="s" style="color: #d14;">"--reference"</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="449" 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="449" 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">@@ -449,7 +449,7 @@ if __name__ == "__main__":</td>
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449
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449
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">genbank_ref1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">gi|"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">giline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"GI:"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">ntdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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451
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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452
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rf</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">xreadlines</span></span><span class="p"><span class="idiff right">()</span>:</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rf</span><span class="p">:</span></span>
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453
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ntdata</span><span class="p">:</span></span>
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454
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<pre style="margin: 0;"> <span id="LC454" 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;">line</span><span class="p">:</span></span>
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">ntdata</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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">@@ -562,20 +562,20 @@ if __name__ == "__main__":</td>
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span></span>
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563
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">17</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="s" style="color: #d14;"><span class="idiff right">"*"</span></span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"SETTINGS:"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">((</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">17</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="s" style="color: #d14;"><span class="idiff">"*"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"SETTINGS:"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"!"</span><span class="p">:</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"refgenome:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"refgenome:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"refgenome:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"autopick"</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"aligner:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">libMUSCLE"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"seqdir:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seqdir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"outdir:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OS:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">OSTYPE</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"threads:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">threads</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">17</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="s" style="color: #d14;"><span class="idiff right">"*"</span></span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"refgenome:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"autopick"</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"aligner:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">libMUSCLE"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"seqdir:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seqdir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"outdir:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OS:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">OSTYPE</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"|-"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"threads:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">threads</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">((</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">17</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="s" style="color: #d14;"><span class="idiff">"*"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff"><<Parsnp started>></span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff"><<Parsnp started>></span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"></span>
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580
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#1)read fasta files (contigs/scaffolds/finished/DBs/dirs)</span></span>
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581
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python"> <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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"-->Reading Genome (asm, fasta) files from </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s..</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">seqdir</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">@@ -618,7 +618,7 @@ if __name__ == "__main__":</td>
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618
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">char</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">special_chars</span><span class="p">:</span></span>
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619
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">char</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"WARNING: File </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s contains a non-supported special character (</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="s" style="color: #d14;"><span class="idiff">) in file name. Please remove if you'd like to include. For best practices see: http://support.apple.com/en-us/HT202808"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">char</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"WARNING: File </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s contains a non-supported special character (</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="s" style="color: #d14;"><span class="idiff">) in file name. Please remove if you'd like to include. For best practices see: http://support.apple.com/en-us/HT202808"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">char</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">nameok</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nameok</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">@@ -640,12 +640,13 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"> <span class="n" style="color: #333;">reflen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">nameok</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">char</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">special_chars</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">char</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"WARNING: File %s contains a non-supported special character (%s) in file name. Please remove if you'd like to include. For best practices see: http://support.apple.com/en-us/HT202808"%(file,char)</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"WARNING: File %s contains a non-supported special character (%s) in file name. Please remove if you'd like to include. For best practices see: http://support.apple.com/en-us/HT202808"%(file,char)</span></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"> <span class="n" style="color: #333;">nameok</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC652" 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;">nameok</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">@@ -657,7 +658,7 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"> <span class="n" style="color: #333;">totlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">xreadlines</span></span><span class="p"><span class="idiff right">()</span>:</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ff</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">">"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">data</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;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC664" 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;">line</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">@@ -673,21 +674,24 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">totlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">20</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">sizediff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">reflen</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">totlen</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sizediff</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.6</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sizediff</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">1.4</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#EDITED THIS TO CHANGE GENOME THRESHOLD, WILL NOW CONSIDER CONCATENATED GENOMES THAT ARE MUCH BIGGER THAN THE REFERENCE</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if sizediff <= 0.6 or sizediff >= 1.4:</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sizediff</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">1.4</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print file #TEST PRINT FOR CHECKING THRESHOLD</span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">fnafiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="python"> <span class="n" style="color: #333;">fnaf_sizes</span><span class="p">[</span><span class="nb" style="color: #0086b3;">file</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">totlen</span><span class="c1" style="color: #998; font-style: italic;">#len(data)</span></span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#sys.exit(1) TEST SYS EXIT FOR CHECKING THRESHOLD</span></span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fnafiles</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="python"> <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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"ERROR: reference genome </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s also in genome directory, restart and select different reference genome</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"!"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;">fnafiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#sort reference by largest replicon to smallest</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sortem</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">autopick_ref</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python"> <span class="n" style="color: #333;">ff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span><span class="s" style="color: #d14;">'r'</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">@@ -703,7 +707,7 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span><span class="p">[</span><span class="n" style="color: #333;">hdr</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nt</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"> <span class="n" style="color: #333;">seq_len</span><span class="p">[</span><span class="n" style="color: #333;">hdr</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="python"> <span class="n" style="color: #333;">seq_len_sort</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;"><span class="idiff left">seq_len</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">iteritems</span></span><span class="p"><span class="idiff right">(</span>),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="python"> <span class="n" style="color: #333;">seq_len_sort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">iter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq_len</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">()</span>),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;">seq_len_sort</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reverse</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"> <span class="n" style="color: #333;">ffo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".ref"</span><span class="p">),</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">item</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_len_sort</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">@@ -714,7 +718,7 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".ref"</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genbank_ref</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> </span>
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#remove any query sequences 30% diff in length</span></span>
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719
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"> <span class="n" style="color: #333;">allfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span></span>
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720
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#write INI file</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="763" 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="767" 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">@@ -763,7 +767,8 @@ if __name__ == "__main__":</td>
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763
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767
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<pre style="margin: 0;"> <span id="LC767" 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;">inifile_exists</span><span class="p">:</span></span>
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764
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fnafiles</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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765
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<td class="diff-line-num new_line" data-linenumber="769" 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">
769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"> <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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"Parsnp requires 2 or more genomes to run, exiting</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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766
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">fnafiles</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">fnafiles</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' '</span><span class="p">)</span> </span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span></span>
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767
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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768
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"> </span>
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769
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="python"> <span class="n" style="color: #333;">file_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="792" 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="797" 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">@@ -792,7 +797,7 @@ if __name__ == "__main__":</td>
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792
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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793
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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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794
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<td class="diff-line-num new_line" data-linenumber="799" 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">
799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="python"> <span class="n" style="color: #333;">mumif</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"all.mumi"</span><span class="p">,</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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795
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mumif</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">xreadlines</span></span><span class="p"><span class="idiff right">()</span>:</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mumif</span><span class="p">:</span></span>
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796
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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797
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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798
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="python"> <span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">mi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="809" 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">@@ -804,13 +809,13 @@ if __name__ == "__main__":</td>
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804
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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805
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fnafiles</span><span class="p">:</span></span>
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806
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python"> <span class="n" style="color: #333;">mumi_dict</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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807
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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808
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"> <span class="n" style="color: #333;">finalfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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809
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"> <span class="n" style="color: #333;">lowest_mumi</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span></span>
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810
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"> <span class="n" style="color: #333;">auto_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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811
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="python"></span>
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812
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817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">autopick_ref</span><span class="p">:</span></span>
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813
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">mumi_dict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">(</span>):</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mumi_dict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">()</span>):</span></span>
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814
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mumi_dict</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lowest_mumi</span><span class="p">:</span></span>
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815
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="python"> <span class="n" style="color: #333;">auto_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqdir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fnafiles</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span></span>
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816
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821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">auto_ref</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="826" 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="831" 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">@@ -826,9 +831,9 @@ if __name__ == "__main__":</td>
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826
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">mumi_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"recruited_genomes.lst"</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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827
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="python"> </span>
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828
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">VERBOSE</span><span class="p">:</span></span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"RECRUITED GENOMES:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"RECRUITED GENOMES:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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830
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="python"></span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">sorted_x</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;"><span class="idiff left">mumi_dict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">iteritems</span></span><span class="p"><span class="idiff right">(</span>),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="python"> <span class="n" style="color: #333;">sorted_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">iter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mumi_dict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">()</span>),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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832
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="python"> <span class="n" style="color: #333;">scnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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833
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">mumivals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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834
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839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">item</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sorted_x</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">@@ -859,11 +864,11 @@ if __name__ == "__main__":</td>
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859
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mumi_only</span><span class="p">:</span></span>
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860
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">mumi_f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">seqdir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fnafiles</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">",</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">mumi_dict</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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861
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">VERBOSE</span><span class="p">:</span></span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">fnafiles</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">idx</span></span><span class="p"><span class="idiff right">]</span></span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">fnafiles</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">idx</span></span><span class="p"><span class="idiff right">])</span></span></span>
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863
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python"> <span class="n" style="color: #333;">finalfiles</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;">fnafiles</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">])</span></span>
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864
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python"> <span class="n" style="color: #333;">allfiles</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;">fnafiles</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">])</span></span>
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865
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">VERBOSE</span><span class="p">:</span></span>
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866
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="python"></span>
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868
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">curated</span><span class="p">:</span></span>
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869
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fnafiles</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">@@ -947,7 +952,7 @@ if __name__ == "__main__":</td>
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947
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952
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<pre style="margin: 0;"> <span id="LC952" class="line" lang="python"> </span>
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948
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="python"></span>
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949
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#3)run parsnp (cores, grid?)</span></span>
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950
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-->Running Parsnp multi-MUM search and libMUSCLE aligner.."</span></span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-->Running Parsnp multi-MUM search and libMUSCLE aligner.."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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951
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956
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<pre style="margin: 0;"> <span id="LC956" 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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"blocks"</span><span class="p">):</span></span>
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952
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"blocks"</span><span class="p">)</span></span>
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1001" 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">@@ -996,7 +1001,7 @@ if __name__ == "__main__":</td>
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996
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="python"> <span class="n" style="color: #333;">totseqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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997
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1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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998
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1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="python"> <span class="n" style="color: #333;">cf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnpAligner.log"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> </span>
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999
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cf</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">xreadlines</span></span><span class="p"><span class="idiff right">()</span>:</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cf</span><span class="p">:</span></span>
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1000
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Total coverage among all sequences:"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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1001
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1006
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="python"> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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1002
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1007
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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="python"> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">))</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">100.0</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">@@ -1004,7 +1009,7 @@ if __name__ == "__main__":</td>
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1004
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="python"> <span class="n" style="color: #333;">totlength</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"bps"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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1005
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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="python"> <span class="n" style="color: #333;">totseqs</span> <span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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1006
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">:</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"parsnpAligner.log missing, parsnpAligner failed, exiting.."</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"parsnpAligner.log missing, parsnpAligner failed, exiting.."</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1008
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1009
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="python"></span>
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1010
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#update thresholds</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1020" 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">@@ -1015,10 +1020,10 @@ if __name__ == "__main__":</td>
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1015
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="python"> <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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">" |->["</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">WARNING_YELLOW</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"WARNING"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ENDC</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"]"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">": aligned regions cover less than 10</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">of reference genome! please verify recruited genomes are all strain of interest"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ENDC</span><span class="p">)</span></span>
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1016
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1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1017
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1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1019
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="python"> <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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1020
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="python"> <span class="n" style="color: #333;">elapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">t2</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">t1</span><span class="p">)</span></span>
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1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"-->Getting list of LCBs.."</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"-->Getting list of LCBs.."</span></span>
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1022
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<td class="diff-line-num new_line" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="python"> <span class="n" style="color: #333;">allbfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"blocks/b*/*"</span><span class="p">)</span></span>
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1023
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="python"> <span class="n" style="color: #333;">blockfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1024
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="python"> <span class="n" style="color: #333;">icnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1060" 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="1065" 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">@@ -1060,7 +1065,7 @@ if __name__ == "__main__":</td>
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1060
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="python"> <span class="n" style="color: #333;">recombination_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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1061
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1066
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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="python"> <span class="n" style="color: #333;">bedfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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1062
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1067
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<pre style="margin: 0;"> <span id="LC1067" class="line" lang="python"> <span class="n" style="color: #333;">bedfile_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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1063
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<td class="diff-line-num new_line old" data-linenumber="1068" 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="LC1063" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-->Running PhiPack on LCBs to detect recombination.."</span></span></span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-->Running PhiPack on LCBs to detect recombination.."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1064
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run_recomb_filter</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">blockfiles</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1065
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1070
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="python"></span>
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1066
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1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="python"> <span class="n" style="color: #333;">bedfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/parsnp.rec"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">),</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1091" 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="1096" 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">@@ -1091,7 +1096,7 @@ if __name__ == "__main__":</td>
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1091
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1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="python"> </span>
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1092
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1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#run parallelPhiPack</span></span>
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1093
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="python"> <span class="n" style="color: #333;">pool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Pool</span><span class="p">(</span><span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">))</span></span>
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1094
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">map_async</span><span class="p">(</span><span class="n" style="color: #333;">parallelPhiWrapper</span><span class="p">,</span><span class="n" style="color: #333;">tasks</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max<span class="idiff left right">int</span></span><span class="p">)</span></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">map_async</span><span class="p">(</span><span class="n" style="color: #333;">parallelPhiWrapper</span><span class="p">,</span><span class="n" style="color: #333;">tasks</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max<span class="idiff left right">size</span></span><span class="p">)</span></span>
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1095
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1100
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="python"> </span>
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1096
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1101
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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">:</span></span>
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1097
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="s" style="color: #d14;">"status"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1126" 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="1131" 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">@@ -1126,7 +1131,7 @@ if __name__ == "__main__":</td>
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1126
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="python"> <span class="n" style="color: #333;">bedfile_dict</span><span class="p">[</span><span class="n" style="color: #333;">srpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">REC</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.3</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">srpos</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">block_spos</span><span class="p">,</span><span class="nb" style="color: #0086b3;">eval</span><span class="p">)</span></span>
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1127
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1128
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="python"> <span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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1129
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<pre style="margin: 0;">-<span id="LC1129" class="line" lang="python"> <span class="n" style="color: #333;">chr_spos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ref_seqs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1130" 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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1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="python"> <span class="n" style="color: #333;">chr_spos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ref_seqs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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1130
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<td class="diff-line-num new_line" data-linenumber="1135" 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">
1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chr_spos</span><span class="p">:</span></span>
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1131
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">block_spos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">chr_spos</span><span class="p">:</span></span>
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1132
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1137
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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="python"> <span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_seqs</span><span class="p">[</span><span class="n" style="color: #333;">cs</span><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1142" 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="1147" 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">@@ -1142,7 +1147,7 @@ if __name__ == "__main__":</td>
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1142
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="python"></span>
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1143
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1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="python"> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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1144
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1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="python"> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">()</span></span>
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1145
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<pre style="margin: 0;">-<span id="LC1145" class="line" lang="python"> <span class="n" style="color: #333;">brkeys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">bedfile_dict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="python"> <span class="n" style="color: #333;">brkeys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bedfile_dict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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1146
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1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="python"> <span class="n" style="color: #333;">brkeys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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1147
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1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">brkeys</span><span class="p">:</span></span>
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1148
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1153
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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="python"> <span class="n" style="color: #333;">bedfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">bedfile_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1178" 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">@@ -1173,20 +1178,20 @@ if __name__ == "__main__":</td>
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1173
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1178
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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/harvest -q -i </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/parsnp.ggr -S "</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">PARSNP_DIR</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks"</span><span class="p">)</span></span>
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="python"></span>
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/ft -nt -quote -gamma -slow -boot 100 "</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">PARSNP_DIR</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks > "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span></span>
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1176
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<td class="diff-line-num new_line old" data-linenumber="1181" 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="LC1176" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-->Reconstructing core genome phylogeny.."</span></span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-->Reconstructing core genome phylogeny.."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1177
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1182
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<pre style="margin: 0;"> <span id="LC1182" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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1178
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1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#7)reroot to midpoint</span></span>
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1179
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"outtree"</span><span class="p">):</span></span>
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1180
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"rm outtree"</span><span class="p">)</span></span>
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1181
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="python"> </span>
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1187
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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reroot_tree</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">finalfiles</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right"> </span>"-->Midpoint reroot.."</span></span>
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print<span class="idiff left right">(</span>"-->Midpoint reroot.."</span></span>
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1184
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1189
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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1190
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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="python"> <span class="n" style="color: #333;">mtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">),</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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1186
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1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="python"> <span class="n" style="color: #333;">mtreedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="python"> <span class="n" style="color: #333;">mtreedata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="python"> <span class="n" style="color: #333;">mtreedata</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mtreedata</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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1193
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<pre style="margin: 0;"> <span id="LC1193" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_from_string</span><span class="p">(</span><span class="n" style="color: #333;">mtreedata</span><span class="p">,</span><span class="s" style="color: #d14;">"newick"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reroot_at_midpoint</span><span class="p">(</span><span class="n" style="color: #333;">update_<span class="idiff left right">split</span>s</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reroot_at_midpoint</span><span class="p">(</span><span class="n" style="color: #333;">update_<span class="idiff left right">bipartition</span>s</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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1190
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1195
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<pre style="margin: 0;"> <span id="LC1195" class="line" lang="python"> <span class="n" style="color: #333;">mftreef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">as_string</span><span class="p">(</span><span class="s" style="color: #d14;">'newick'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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1191
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1196
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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print mftreef</span></span>
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1192
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1197
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="python"> <span class="n" style="color: #333;">mtreef</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.final.tree"</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1195" 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="1200" 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">@@ -1195,25 +1200,25 @@ if __name__ == "__main__":</td>
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1195
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1200
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.final.tree"</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span><span class="p">))</span></span>
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1196
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">:</span></span>
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1197
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1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="python"> <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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"ERROR: cannot process fasttree output, skipping midpoint reroot..</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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1198
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<pre style="margin: 0;">-<span id="LC1198" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1199
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1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="python"></span>
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1200
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1205
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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="python"></span>
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1201
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1206
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">use_gingr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1202
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<pre style="margin: 0;">-<span id="LC1202" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-->Creating Gingr input file.."</span></span></span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-->Creating Gingr input file.."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1203
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1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">xtrafast</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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1204
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1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if newick available, add</span></span>
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1205
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1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new flag to update branch lengths</span></span>
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1206
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1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/harvest --midpoint-reroot -u -q -i "</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">PARSNP_DIR</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.ggr -o "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.ggr -n </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree "</span><span class="p">))</span></span>
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1207
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="python"> </span>
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1208
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<pre style="margin: 0;">-<span id="LC1208" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" |->["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="python"></span>
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1210
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<pre style="margin: 0;">-<span id="LC1210" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-->Calculating wall clock time.. "</span></span></span>
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1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-->Calculating wall clock time.. "</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">elapsed</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="mf" style="color: #099;">60.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60</span><span class="p">:</span></span>
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1212
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<pre style="margin: 0;">-<span id="LC1212" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" |->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Aligned </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d genomes in </span></span><span class="si" style="color: #d14;"><span class="idiff">%.2</span></span><span class="s" style="color: #d14;"><span class="idiff">f hours"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">totseqs</span></span><span class="p"><span class="idiff">,</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">elapsed</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="mf" style="color: #099;"><span class="idiff">3600.0</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" |->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Aligned </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d genomes in </span></span><span class="si" style="color: #d14;"><span class="idiff">%.2</span></span><span class="s" style="color: #d14;"><span class="idiff">f hours"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">totseqs</span></span><span class="p"><span class="idiff">,</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">elapsed</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="mf" style="color: #099;"><span class="idiff">3600.0</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1213
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1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">elapsed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60</span><span class="p">:</span></span>
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1214
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<pre style="margin: 0;">-<span id="LC1214" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" |->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Aligned </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d genomes in </span></span><span class="si" style="color: #d14;"><span class="idiff">%.2</span></span><span class="s" style="color: #d14;"><span class="idiff">f minutes"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">totseqs</span></span><span class="p"><span class="idiff">,</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">elapsed</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="mf" style="color: #099;"><span class="idiff">60.0</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" |->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Aligned </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d genomes in </span></span><span class="si" style="color: #d14;"><span class="idiff">%.2</span></span><span class="s" style="color: #d14;"><span class="idiff">f minutes"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">totseqs</span></span><span class="p"><span class="idiff">,</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">elapsed</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="mf" style="color: #099;"><span class="idiff">60.0</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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1216
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<pre style="margin: 0;">-<span id="LC1216" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" |->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Aligned </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d genomes in </span></span><span class="si" style="color: #d14;"><span class="idiff">%.2</span></span><span class="s" style="color: #d14;"><span class="idiff">f seconds"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">totseqs</span></span><span class="p"><span class="idiff">,</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">elapsed</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" |->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Aligned </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d genomes in </span></span><span class="si" style="color: #d14;"><span class="idiff">%.2</span></span><span class="s" style="color: #d14;"><span class="idiff">f seconds"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">totseqs</span></span><span class="p"><span class="idiff">,</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">elapsed</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1217
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#cleanup</span></span>
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1218
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1223
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<pre style="margin: 0;"> <span id="LC1223" class="line" lang="python"> <span class="n" style="color: #333;">rmfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"*.aln"</span><span class="p">)</span></span>
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1219
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<td class="diff-line-num new_line" data-linenumber="1224" 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">
1224
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<pre style="margin: 0;"> <span id="LC1224" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#rmfiles2 = glob.glob(outputDir+os.sep+"blocks/b*/*")</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1224" 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>
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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">@@ -1224,33 +1229,33 @@ if __name__ == "__main__":</td>
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1224
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1229
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<pre style="margin: 0;"> <span id="LC1229" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"rm -rf </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">))</span></span>
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1225
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1230
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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="python"></span>
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1226
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1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="python"> <span class="n" style="color: #333;">filepres</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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1227
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<pre style="margin: 0;">-<span id="LC1227" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff"><<Parsnp finished! All output available in </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s>>"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1228
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<pre style="margin: 0;">-<span id="LC1228" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span></span>
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1229
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<td class="diff-line-num new_line old" data-linenumber="1232" 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="LC1229" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Validating output directory contents..."</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1230
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<td class="diff-line-num new_line old" data-linenumber="1232" 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="LC1230" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">1)parsnp.tree:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">newick format tree"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">,</span></span></span>
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1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff"><<Parsnp finished! All output available in </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s>>"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outputDir</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Validating output directory contents..."</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">1)parsnp.tree:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">newick format tree"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">' '</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1231
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1236
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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1232
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<pre style="margin: 0;">-<span id="LC1232" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1233
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1238
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<pre style="margin: 0;"> <span id="LC1238" class="line" lang="python"> <span class="n" style="color: #333;">filepres</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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1234
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1239
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<pre style="margin: 0;"> <span id="LC1239" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1235
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">|->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"MISSING"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1236
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<td class="diff-line-num new_line old" data-linenumber="1240" 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="LC1236" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">2)parsnp.ggr:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">harvest input file for gingr (GUI)"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">,</span></span></span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">|->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"MISSING"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">2)parsnp.ggr:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">harvest input file for gingr (GUI)"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">' '</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1237
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnp.ggr"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnp.ggr"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1238
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<pre style="margin: 0;">-<span id="LC1238" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1239
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="python"> <span class="n" style="color: #333;">filepres</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1241
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<pre style="margin: 0;">-<span id="LC1241" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">|->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"MISSING"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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1242
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<pre style="margin: 0;">-<span id="LC1242" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">3)parsnp.xmfa:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">XMFA formatted multi-alignment"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">,</span></span></span>
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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">|->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"MISSING"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">BOLDME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">3)parsnp.xmfa:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">XMFA formatted multi-alignment"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</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">' '</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnp.xmfa"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sparsnp.xmfa"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1244" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">OK_GREEN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"OK"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="python"> <span class="n" style="color: #333;">filepres</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1247" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">|->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"MISSING"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff right">ENDC</span></span></span>
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">|->"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"MISSING"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1253
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<pre style="margin: 0;"> <span id="LC1253" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filepres</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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1254
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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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1255
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="python"></span>
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1256
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1252
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<td class="diff-line-num new_line old" data-linenumber="1257" 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="LC1252" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Output files missing, something went wrong. Check logs and relaunch or contact developers for assistance"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"]"</span></span></span>
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1253
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<td class="diff-line-num new_line old" data-linenumber="1257" 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="LC1253" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span></span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">["</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ERROR_RED</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"Output files missing, something went wrong. Check logs and relaunch or contact developers for assistance"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">ENDC</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1258" 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">
1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1254
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<td class="diff-line-num new_line" data-linenumber="1259" 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">
1259
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<pre style="margin: 0;"> <span id="LC1259" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sblocks"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">)):</span></span>
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1255
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<td class="diff-line-num new_line" data-linenumber="1260" 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">
1260
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<pre style="margin: 0;"> <span id="LC1260" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">sblocks"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span></span>
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1256
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<td class="diff-line-num new_line" data-linenumber="1261" 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">
1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"allmums.out"</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1294" 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="1299" 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">@@ -1294,6 +1299,6 @@ if __name__ == "__main__":</td>
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1294
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<td class="diff-line-num new_line" data-linenumber="1299" 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">
1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#check if available first</span></span>
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1295
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1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="python"> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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1296
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">binary_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"osx"</span><span class="p">:</span></span>
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1297
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<td class="diff-line-num new_line old" data-linenumber="1302" 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="LC1297" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">">>Launching gingr.."</span></span></span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">">>Launching gingr.."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1298
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<td class="diff-line-num new_line" data-linenumber="1303" 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">
1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"open -n </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s --args </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/parsnp.ggr"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">use_gingr</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="p">))</span></span>
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1299
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1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="python"></span></pre>
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<li id="84bc0ed2d88b3c731434e92eda347d97bd9d28cf">
<a href="https://salsa.debian.org/med-team/parsnp/commit/39bab4561e3395ce3315c468c2d6c09e2830b1fa#84bc0ed2d88b3c731434e92eda347d97bd9d28cf"><strong>build_parsnp_linux.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,4 +5,6 @@ make install</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell">./autogen.sh</span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell">./configure</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Fix MUSCLE-3.7 linker"</span> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">make <span class="nv" style="color: #008080;">LDADD</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-lMUSCLE-3</span>.7</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell">make <span class="nb" style="color: #0086b3;">install</span></span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/commit/39bab4561e3395ce3315c468c2d6c09e2830b1fa#7aed50886f48c76682f73aa91239f317031d0670"><strong>build_parsnp_osx.sh</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">@@ -7,4 +7,6 @@ make install</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell">./autogen.sh</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell">./configure</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Fix MUSCLE-3.7 linker"</span> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">make <span class="nv" style="color: #008080;">LDADD</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-lMUSCLE-3</span>.7</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell">make <span class="nb" style="color: #0086b3;">install</span></span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/commit/39bab4561e3395ce3315c468c2d6c09e2830b1fa#f70362ee3b338a3c3a0b866ec092e0439c9d019c"><strong>install.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span><span class="n" style="color: #333;">sys</span><span class="p">,</span><span class="n" style="color: #333;">string</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#parsnp basic INSTALL script</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">user_home</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">"HOME"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<<Welcome to Parsnp utility script install>>"</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"<<Welcome to Parsnp utility script install>>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#check for python version</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">version_info</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">version_info</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">6</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left">3</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">version_info</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">version_info</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"Python version is </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Parsnp requires at least 2.6"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">version</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Python version is </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Parsnp requires at least 3.1"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#complete shebang</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">@@ -16,4 +16,4 @@ scripts = ["parsnp.py"]</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#copy to currdir</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">script</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">scripts</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">script</span><span class="p">,</span><span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">".py"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)))</span></span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">script</span><span class="p">,</span><span class="n" style="color: #333;">script</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">".py"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/commit/39bab4561e3395ce3315c468c2d6c09e2830b1fa#2e8ce15c0b817fa44897094ab9c5f2c504a96ccd"><strong>script/shuffle.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +51,7 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">rnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">shuffleperseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">Usage: shuffleGenome <FastA input file> <output file> <Rearrangement size> <Number of rearrangements> <Shuffled sequences per seq>"</span></span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Usage: shuffleGenome <FastA input file> <output file> <Rearrangement size> <Number of rearrangements> <Shuffled sequences per seq>"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">infileName</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;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</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">@@ -77,22 +77,22 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">infiled</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">filelen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">infiled</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Input sequence:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="n" style="color: #333;"><span class="idiff right">seqfile</span></span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"Input sequence length: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="n" style="color: #333;"><span class="idiff right">filelen</span></span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Input sequence:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="n" style="color: #333;"><span class="idiff">seqfile</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Input sequence length: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="n" style="color: #333;"><span class="idiff">filelen</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#split genome into filelen/rsize parts</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">partlist</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rsize</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">filelen</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">rsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filelen</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">part</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">filelen</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rsize</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">part</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">filelen</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rsize</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">partlist</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;">infiled</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">:(</span><span class="n" style="color: #333;">part</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rsize</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">rsize</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">partlist</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;">infiled</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">:])</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">shuffleit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">shuffleperseq</span><span class="p">):</span> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">shuffleit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">shuffleperseq</span><span class="p">):</span> </span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">seq</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="LC98" class="line" lang="python"> <span class="n" style="color: #333;">parttemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</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">@@ -114,13 +114,13 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">parttemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partlist</span><span class="p">[</span><span class="n" style="color: #333;">part1</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">partlist</span><span class="p">[</span><span class="n" style="color: #333;">part1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partlist</span><span class="p">[</span><span class="n" style="color: #333;">part2</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">partlist</span><span class="p">[</span><span class="n" style="color: #333;">part2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parttemp</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"Transposition"</span></span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" Positions </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d swapped"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">part1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">part2</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Transposition"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" Positions </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d swapped"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">part1</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">part2</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">operation</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#inversion</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">partlist</span><span class="p">[</span><span class="n" style="color: #333;">part1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">invertSeq</span><span class="p">(</span><span class="n" style="color: #333;">partlist</span><span class="p">[</span><span class="n" style="color: #333;">part1</span><span class="p">])</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"Inversion"</span></span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">" Position </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="n" style="color: #333;"><span class="idiff right">part1</span></span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Inversion"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" Position </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="n" style="color: #333;"><span class="idiff">part1</span></span><span class="p"><span class="idiff right">)</span></span></span>
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124
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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125
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"></span>
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126
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" 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="137" 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">@@ -137,7 +137,7 @@ if __name__ == "__main__":</td>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#write output to file</span></span>
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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqfile</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"_Shuffled_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d.fna"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">shuffleit</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"output: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fname</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"output: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fname</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> </span>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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143
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">fout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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