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<h3>
Andreas Tille pushed to branch master
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/ed761e73cfc48d311094c7017ebbf17c38072e23">ed761e73</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T13:01:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/commit/d2555b509953a685db427d1529477abd767c6fb8">d2555b50</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T13:06:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2+dfsg</pre>
</li>
<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>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/commit/a0bcd60a243e242e4e3a21d4223a1e433ca209da">a0bcd60a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-14T10:17:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/commit/002dd92e5ab41211c0afd573ec8cca9ceee92350">002dd92e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-14T10:17:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.1+dfsg'
Update to upstream version '1.2.1+dfsg'
with Debian dir 7ef626f49e7941e722d0ee2024a1ebcefc43d9b2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/commit/ded87a13e7cd6c4c73ceebf1835280cbc40dfd0a">ded87a13</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-14T10:17:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/commit/ebdfd433b0f28c0d0dfb0bdf09f5a0b27f5edaa8">ebdfd433</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-14T10:26:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/commit/87af9db0b3b158ad7e42635f52a1e138cf988260">87af9db0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-14T10:29:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
</a>
</li>
<li class="file-stats">
<a href="#50e9f8fb17151457a31901c72f33d2bcafa9e1a1">
Parsnp.py
</a>
</li>
<li class="file-stats">
<a href="#84bc0ed2d88b3c731434e92eda347d97bd9d28cf">
build_parsnp_linux.sh
</a>
</li>
<li class="file-stats">
<a href="#7aed50886f48c76682f73aa91239f317031d0670">
build_parsnp_osx.sh
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#85f404a0760e49ec237056c4b1f037904e9e3a67">
debian/patches/2to3_new.patch
</a>
</li>
<li class="file-stats">
<a href="#82bdf410ee3abb85c057e0147f43e488d2f00daf">
debian/patches/proper_calls_to_tools.patch
</a>
</li>
<li class="file-stats">
<a href="#f70362ee3b338a3c3a0b866ec092e0439c9d019c">
install.py
</a>
</li>
<li class="file-stats">
<a href="#2e8ce15c0b817fa44897094ab9c5f2c504a96ccd">
script/shuffle.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">
<a href="https://salsa.debian.org/med-team/parsnp/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#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="LC9" class="line" lang="plaintext"></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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18
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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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3
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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4
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20
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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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5
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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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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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7
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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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8
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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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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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10
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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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11
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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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12
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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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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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14
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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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15
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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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16
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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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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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24
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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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25
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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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26
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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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27
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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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<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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">met:</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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24
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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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25
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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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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27
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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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28
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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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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">documentation and/or other materials provided with the distribution.</span>
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31
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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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32
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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="LC34" class="line" lang="plaintext"></span>
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35
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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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36
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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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37
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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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38
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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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39
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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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<td class="diff-line-num new old_line" data-linenumber="28" 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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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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<td class="diff-line-num new old_line" data-linenumber="28" 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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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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<td class="diff-line-num new old_line" data-linenumber="28" 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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43
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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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<td class="diff-line-num new old_line" data-linenumber="28" 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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44
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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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45
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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/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#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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<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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<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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="243" 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">
243
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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="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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<td class="diff-line-num old old_line" data-linenumber="244" 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">
244
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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="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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245
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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="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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="246" 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">
246
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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="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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<td class="diff-line-num old old_line" data-linenumber="247" 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">
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>
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248
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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="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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<td class="diff-line-num old old_line" data-linenumber="249" 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">
249
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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="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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="250" 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">
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>
</pre>
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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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<td class="diff-line-num old old_line" data-linenumber="254" 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">
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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="256" 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">
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>
</pre>
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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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<td class="diff-line-num old old_line" data-linenumber="258" 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">
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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<td class="diff-line-num old old_line" data-linenumber="260" 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">
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>
</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="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 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="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 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="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>
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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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<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="243" 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">
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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<td class="diff-line-num new new_line" data-linenumber="245" 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">
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 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="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>
</pre>
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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 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="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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<td class="diff-line-num new new_line" data-linenumber="250" 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">
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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<td class="diff-line-num new new_line" data-linenumber="255" 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">
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 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="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>
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261
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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>
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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>
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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="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="idiff right"> </span></span>
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264
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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="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 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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<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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<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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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="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>
</pre>
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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>
</pre>
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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>
</pre>
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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>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
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>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
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>
</pre>
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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>
</pre>
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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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="275" 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">
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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="277" 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="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>
</pre>
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277
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<td class="diff-line-num new_line" data-linenumber="277" 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">
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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="278" 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">
278
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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>
</pre>
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279
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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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<td class="diff-line-num old old_line" data-linenumber="280" 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">
280
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="281" 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">
281
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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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<td class="diff-line-num old old_line" data-linenumber="282" 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">
282
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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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<td class="diff-line-num old old_line" data-linenumber="283" 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">
283
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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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<td class="diff-line-num old old_line" data-linenumber="284" 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">
284
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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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<td class="diff-line-num old old_line" data-linenumber="285" 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">
285
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="286" 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">
286
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<td class="diff-line-num new_line old" data-linenumber="278" 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="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 old_line" data-linenumber="287" 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="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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<td class="diff-line-num new old_line" data-linenumber="287" 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="279" 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">
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 old_line" data-linenumber="287" 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">
</td>
<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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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>
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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="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>
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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="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>
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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="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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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="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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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"></span>
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288
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288
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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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289
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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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291
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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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292
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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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293
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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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289
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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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291
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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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292
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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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293
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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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294
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"></span>
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295
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"></span>
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296
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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>
<td class="diff-line-num unfold js-unfold new_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>
<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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301
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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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<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="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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<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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450
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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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<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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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="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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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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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> </span>
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621
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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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622
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622
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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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623
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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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624
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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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718
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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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717
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> </span>
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718
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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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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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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 old_line" data-linenumber="804" 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="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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867
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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="diff-line-num unfold js-unfold old_line" data-linenumber="947" 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="952" 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">@@ -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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953
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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="diff-line-num unfold js-unfold new_line" data-linenumber="1009" 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">@@ -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 old_line" data-linenumber="1015" 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="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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<td class="diff-line-num new_line" data-linenumber="1028" 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">
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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<td class="diff-line-num new_line" data-linenumber="1097" 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">
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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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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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="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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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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1174
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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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1175
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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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1182
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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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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;">#print<span class="idiff left right"> </span>"-->Midpoint reroot.."</span></span>
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1188
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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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1187
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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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1188
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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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1189
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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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<td class="diff-line-num new_line" data-linenumber="1206" 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">
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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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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<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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<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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1215
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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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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="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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<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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<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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<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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<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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<td class="diff-line-num new_line old" data-linenumber="1237" 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="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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<td class="diff-line-num new new_line" data-linenumber="1241" 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">
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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<td class="diff-line-num new_line old" data-linenumber="1243" 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="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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<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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<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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<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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<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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<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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<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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<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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<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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1249
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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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1250
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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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1251
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<td class="diff-line-num new_line" data-linenumber="1256" 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">
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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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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<td class="diff-line-num new_line" data-linenumber="1300" 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">
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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<td class="diff-line-num new_line" data-linenumber="1301" 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">
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/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#84bc0ed2d88b3c731434e92eda347d97bd9d28cf"><strong>build_parsnp_linux.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">@@ -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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell">./autogen.sh</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell">./configure</span>
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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/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#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/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">parsnp (1.2.1+dfsg-1) unstable; urgency=medium</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"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 14 Nov 2019 11:27:23 +0100</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">parsnp (1.2+dfsg-6) unstable; urgency=medium</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"> * Use 2to3 to port to Python3</span>
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<a href="https://salsa.debian.org/med-team/parsnp/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> cython3,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libmuscle-dev</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/parsnp</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/parsnp.git</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html</span>
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<li id="85f404a0760e49ec237056c4b1f037904e9e3a67">
<a href="https://salsa.debian.org/med-team/parsnp/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#85f404a0760e49ec237056c4b1f037904e9e3a67"><strong>debian/patches/2to3_new.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/937242</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Fri, 13 Sep 2019 12:08:17 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Thu, 14 Nov 2019 11:25:23 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Remark: Upstream claimed to have applied the 2to3 patch but the</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> remaining iteritems looks suspicious and thus the patch is remaining</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> here.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff">--- a/Parsnp.py</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Parsnp.py</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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">@@ -11,307 +14,7 @@ Last-Update: Fri, 13 Sep 2019 12:08:17 +0200</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> # See the LICENSE file included with this software for license information.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> import os, sys, string, getopt, random,subprocess, time, glob,operator, math, datetime,numpy #pysam</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -94,7 +94,7 @@</span> else:</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> def handler(signum, frame):</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> global SIGINT</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> SIGINT = True</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Caught request to terminate by user (CTRL+C), exiting now, bye'</span></span>
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19
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Caught request to terminate by user (CTRL+C), exiting now, bye')</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> sys.exit(128)</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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">
22
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC22" class="line" lang="diff"> signal.signal(signal.SIGINT, handler)</span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC23" class="line" lang="diff"><span class="p">@@ -218,79 +218,79 @@</span> if os.path.exists("%s/MUMmer/nucmer_run"</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">
24
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<td class="diff-line-num new_line old" data-linenumber="17" 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="diff"> ff.close()</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> </span>
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26
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC26" class="line" lang="diff"> def version():</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="27" 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">
27
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print VERSION</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(VERSION)</span></span>
</pre>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
</pre>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> def usage():</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
31
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: parsnp [options] [-g|-r|-q](see below) -d <genome_dir> -p <threads>"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="32" 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">
32
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="33" 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">
33
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Parsnp quick start for three example scenarios: "</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="34" 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">
34
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "1) With reference & genbank file: "</span></span>
</pre>
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35
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " >parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d <genome_dir> -p <threads> "</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="36" 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">
36
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="37" 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">
37
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "2) With reference but without genbank file:"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="38" 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">
38
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " >parsnp -r <reference_genome> -d <genome_dir> -p <threads> "</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="39" 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">
39
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="40" 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">
40
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "3) Autorecruit reference to a draft assembly:"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="41" 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">
41
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " >parsnp -q <draft_assembly> -d <genome_db> -p <threads> "</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="42" 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">
42
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="43" 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">
43
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "[Input parameters]"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="44" 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">
44
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "<<input/output>>"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="45" 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">
45
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -c = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="46" 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">
46
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -d = <path>: (d)irectory containing genomes/contigs/scaffolds"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="47" 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">
47
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -r = <path>: (r)eference genome (set to ! to pick random one from genome dir)"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="48" 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">
48
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -g = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None)"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="49" 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">
49
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -o = <string>: output directory? default [./P_CURRDATE_CURRTIME]"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="50" 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">
50
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="51" 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">
51
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="52" 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">
52
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "<<MUMi>>"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="53" 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">
53
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -U = <float>: max MUMi distance value for MUMi distribution "</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="54" 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">
54
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -M = <flag>: calculate MUMi and exit? overrides all other choices! (default: NO)"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="55" 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">
55
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: parsnp [options] [-g|-r|-q](see below) -d <genome_dir> -p <threads>")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="56" 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">
56
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="57" 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">
57
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Parsnp quick start for three example scenarios: ")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="58" 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">
58
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("1) With reference & genbank file: ")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="59" 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">
59
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" >parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d <genome_dir> -p <threads> ")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="60" 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">
60
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="61" 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">
61
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("2) With reference but without genbank file:")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="62" 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">
62
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" >parsnp -r <reference_genome> -d <genome_dir> -p <threads> ")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="63" 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">
63
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="64" 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">
64
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("3) Autorecruit reference to a draft assembly:")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="65" 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">
65
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" >parsnp -q <draft_assembly> -d <genome_db> -p <threads> ")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="66" 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">
66
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="67" 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">
67
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[Input parameters]")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="68" 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">
68
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("<<input/output>>")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="69" 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">
69
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -c = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="70" 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">
70
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -d = <path>: (d)irectory containing genomes/contigs/scaffolds")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="71" 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">
71
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -r = <path>: (r)eference genome (set to ! to pick random one from genome dir)")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="72" 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">
72
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -g = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None)")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
73
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -o = <string>: output directory? default [./P_CURRDATE_CURRTIME]")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="74" 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">
74
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="75" 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">
75
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="76" 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">
76
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("<<MUMi>>")</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="77" 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">
77
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -U = <float>: max MUMi distance value for MUMi distribution ")</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="78" 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">
78
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -M = <flag>: calculate MUMi and exit? overrides all other choices! (default: NO)")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="79" 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">
79
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC79" class="line" lang="diff"> #new, mutually exclusive</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="80" 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">
80
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -i = <float>: max MUM(i) distance (default: autocutoff based on distribution of MUMi values)"</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="81" 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">
81
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "" </span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="82" 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">
82
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "<<MUM search>>"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="83" 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">
83
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -i = <float>: max MUM(i) distance (default: autocutoff based on distribution of MUMi values)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="84" 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">
84
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("") </span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="85" 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">
85
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("<<MUM search>>")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="86" 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">
86
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> #new, default to lower, 12-17</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="87" 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">
87
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -a = <int>: min (a)NCHOR length (default = 1.1*Log(S))"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="88" 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">
88
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -C = <int>: maximal cluster D value? (default=100)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="89" 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">
89
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -z = <path>: min LCB si(z)e? (default = 25)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="90" 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">
90
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="91" 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">
91
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "<<LCB alignment>>"</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="92" 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">
92
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -D = <float>: maximal diagonal difference? Either percentage (e.g. 0.2) or bp (e.g. 100bp) (default = 0.12)" </span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="93" 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">
93
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -e = <flag> greedily extend LCBs? experimental! (default = NO)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="94" 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">
94
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -n = <string>: alignment program (default: libMUSCLE)" </span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="95" 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">
95
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -u = <flag>: output unaligned regions? .unaligned (default: NO)"</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="96" 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">
96
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="97" 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">
97
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "<<Recombination filtration>>"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="98" 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">
98
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -a = <int>: min (a)NCHOR length (default = 1.1*Log(S))")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="99" 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">
99
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -C = <int>: maximal cluster D value? (default=100)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="100" 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">
100
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -z = <path>: min LCB si(z)e? (default = 25)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="101" 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">
101
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="102" 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">
102
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("<<LCB alignment>>")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="103" 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">
103
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -D = <float>: maximal diagonal difference? Either percentage (e.g. 0.2) or bp (e.g. 100bp) (default = 0.12)") </span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="104" 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">
104
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -e = <flag> greedily extend LCBs? experimental! (default = NO)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="105" 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">
105
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -n = <string>: alignment program (default: libMUSCLE)") </span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="106" 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">
106
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -u = <flag>: output unaligned regions? .unaligned (default: NO)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="107" 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">
107
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="108" 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">
108
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("<<Recombination filtration>>")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="109" 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">
109
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"> #new, default is OFF</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="110" 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">
110
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -x = <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="111" 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">
111
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="112" 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">
112
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "<<Misc>>"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="113" 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">
113
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -h = <flag>: (h)elp: print this message and exit"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="114" 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">
114
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -p = <int>: number of threads to use? (default= 1)"</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="115" 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">
115
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -P = <int>: max partition size? limits memory usage (default= 15000000)"</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="116" 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">
116
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -v = <flag>: (v)erbose output? (default = NO)"</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="117" 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">
117
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -V = <flag>: output (V)ersion and exit"</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="118" 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">
118
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="119" 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">
119
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -x = <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO)")</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="120" 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">
120
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="121" 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">
121
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("<<Misc>>")</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="122" 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">
122
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -h = <flag>: (h)elp: print this message and exit")</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="123" 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">
123
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -p = <int>: number of threads to use? (default= 1)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="124" 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">
124
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -P = <int>: max partition size? limits memory usage (default= 15000000)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="125" 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">
125
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -v = <flag>: (v)erbose output? (default = NO)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="126" 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">
126
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -V = <flag>: output (V)ersion and exit")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="128" 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">
128
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"> </span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="129" 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">
129
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"> #hidden, not yet supported options</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="130" 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">
130
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#print "-q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="131" 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">
131
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#print "-s = <flag>: (s)plit genomes by n's (default = NO)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="132" 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">
132
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#print "-z = <path>: min cluster si(z)e? (default = 10)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="133" 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">
133
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#print "-F = <flag>: fast MUMi calc? (default=NO)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="134" 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">
134
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#print "-g = <bool>: auto-launch (g)ingr? (default = NO)"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="135" 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">
135
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#print("-q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="136" 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">
136
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#print("-s = <flag>: (s)plit genomes by n's (default = NO)")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="137" 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">
137
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#print("-z = <path>: min cluster si(z)e? (default = 10)")</span></span>
</pre>
</td>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#print("-F = <flag>: fast MUMi calc? (default=NO)")</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#print("-g = <bool>: auto-launch (g)ingr? (default = NO)")</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"> </span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"> </span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"> if __name__ == "__main__":</span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"> parsnp_dir= sys.path[0]</span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print parsnp_dir</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print(parsnp_dir)</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"> #PARSNP_DIR = parsnp_dir</span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"> opts = []</span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"> args = []</span>
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<td class="diff-line-num old old_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"> try:</span>
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<td class="diff-line-num old old_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"> opts, args = getopt.getopt(sys.argv[1:], "hxved:C:F:D:i:g:m:MU:o:a:cln:p:P:q:r:Rsz:uV", ["help","xtrafast","verbose","extend","sequencedir","clusterD","DiagonalDiff","iniFile","genbank","mumlength","onlymumi","MUMi","outputDir","anchorlength","curated","layout","aligNmentprog","threads","max-partition-size","query","reference","nofiltreps","split","minclustersiZe","unaligned","version"])</span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except getopt.GetoptError, err:</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except getopt.GetoptError as err:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"> # print help information and exit: </span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print str(err) </span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(str(err)) </span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"> usage()</span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"> sys.exit(2)</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> </span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="p">@@ -346,7 +346,7 @@</span> if __name__ == "__main__":</span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"> usage()</span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"> sys.exit(0)</span>
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<td class="diff-line-num old old_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"> elif o in ("-R","--filtreps"):</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "WARNING: -R option is no longer supported, ignoring. Please see harvest.readthedocs.org for bed filtering w/ harvesttools"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="164" 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">
164
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("WARNING: -R option is no longer supported, ignoring. Please see harvest.readthedocs.org for bed filtering w/ harvesttools")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"> filtreps = False</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="166" 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">
166
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC166" class="line" lang="diff"> elif o in ("-r","--reference"):</span>
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<td class="diff-line-num old old_line" data-linenumber="167" 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">
167
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC167" class="line" lang="diff"> ref = a</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="168" 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">
168
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC168" class="line" lang="diff"><span class="p">@@ -436,7 +436,7 @@</span> if __name__ == "__main__":</span>
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<td class="diff-line-num old old_line" data-linenumber="169" 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">
169
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC169" class="line" lang="diff"> genbank_ref1.write(">gi|"+giline.split("GI:")[-1])</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="170" 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">
170
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC170" class="line" lang="diff"> ntdata = False</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="171" 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">
171
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC171" class="line" lang="diff"> data = ""</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="172" 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">
172
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in rf.xreadlines():</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="173" 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">
173
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in rf:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="174" 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">
174
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC174" class="line" lang="diff"> if ntdata:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="175" 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">
175
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC175" class="line" lang="diff"> if "//" in line:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="176" 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">
176
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC176" class="line" lang="diff"> ntdata = False</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="177" 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">
177
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC177" class="line" lang="diff"><span class="p">@@ -549,20 +549,20 @@</span> if __name__ == "__main__":</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="178" 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">
178
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC178" class="line" lang="diff"> ref = query</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC179" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="180" 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">
180
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"> if 1:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="181" 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">
181
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (len(outputDir)+17)*"*"</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="182" 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">
182
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print BOLDME+"SETTINGS:"+ENDC</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="183" 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">
183
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((len(outputDir)+17)*"*")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="184" 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">
184
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(BOLDME+"SETTINGS:"+ENDC)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="185" 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">
185
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"> if ref != "!":</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="186" 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">
186
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "|-"+BOLDME+"refgenome:\t%s"%(ref)+ENDC</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="187" 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">
187
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("|-"+BOLDME+"refgenome:\t%s"%(ref)+ENDC)</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="188" 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">
188
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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="LC188" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="189" 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">
189
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<td class="diff-line-num new_line old" data-linenumber="17" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "|-"+BOLDME+"refgenome:\t%s"%("autopick")+ENDC</span></span>
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<td class="diff-line-num old old_line" data-linenumber="190" 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">
190
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "|-"+BOLDME+"aligner:\tlibMUSCLE"+ENDC</span></span>
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<td class="diff-line-num old old_line" data-linenumber="191" 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">
191
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "|-"+BOLDME+"seqdir:\t%s"%(seqdir)+ENDC</span></span>
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<td class="diff-line-num old old_line" data-linenumber="192" 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">
192
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "|-"+BOLDME+"outdir:\t%s"%(outputDir)+ENDC</span></span>
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<td class="diff-line-num old old_line" data-linenumber="193" 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">
193
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "|-"+BOLDME+"OS:\t\t%s"%(OSTYPE)+ENDC</span></span>
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<td class="diff-line-num old old_line" data-linenumber="194" 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">
194
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "|-"+BOLDME+"threads:\t%s"%(threads)+ENDC</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="195" 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">
195
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (len(outputDir)+17)*"*"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="196" 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">
196
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("|-"+BOLDME+"refgenome:\t%s"%("autopick")+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="197" 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">
197
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("|-"+BOLDME+"aligner:\tlibMUSCLE"+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="198" 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">
198
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("|-"+BOLDME+"seqdir:\t%s"%(seqdir)+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="199" 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">
199
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("|-"+BOLDME+"outdir:\t%s"%(outputDir)+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="200" 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">
200
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("|-"+BOLDME+"OS:\t\t%s"%(OSTYPE)+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="201" 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">
201
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("|-"+BOLDME+"threads:\t%s"%(threads)+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="202" 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">
202
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((len(outputDir)+17)*"*")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="203" 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">
203
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="204" 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">
204
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n<<Parsnp started>>\n"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="205" 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">
205
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n<<Parsnp started>>\n")</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="206" 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">
206
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC206" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="207" 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">
207
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"> #1)read fasta files (contigs/scaffolds/finished/DBs/dirs)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="208" 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">
208
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"> sys.stderr.write( "-->Reading Genome (asm, fasta) files from %s..\n"%(seqdir))</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="209" 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">
209
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="p">@@ -605,7 +605,7 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="210" 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">
210
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"> for char in special_chars:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="211" 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">
211
</td>
<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"> if char in file:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="212" 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">
212
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"> </span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="214" 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">
214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="215" 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">
215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"> nameok = False</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="216" 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">
216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"> break</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="217" 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">
217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"> if nameok:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="218" 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">
218
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC218" class="line" lang="diff"><span class="p">@@ -632,7 +632,7 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="219" 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">
219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="220" 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">
220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"> for char in special_chars:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="221" 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">
221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"> if char in file:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="222" 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">
222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print "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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="223" 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">
223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print("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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="224" 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">
224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"> nameok = False</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="225" 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">
225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"> break</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="226" 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">
226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"> if not nameok:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="227" 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">
227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff"><span class="p">@@ -644,7 +644,7 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="228" 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">
228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"> data = []</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="230" 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">
230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"> totlen = 0</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="231" 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">
231
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in ff.xreadlines():</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="232" 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">
232
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in ff:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="233" 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">
233
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff"> if line[0] != ">":</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="234" 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">
234
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"> data.append(line.replace("\n",""))</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="235" 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">
235
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff"> if "-" in line:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="236" 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">
236
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<td class="diff-line-num new_line old" data-linenumber="17" 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">
</td>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"><span class="p">@@ -690,7 +690,7 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num old old_line" 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">
237
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC237" class="line" lang="diff"> continue</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="238" 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">
238
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC238" class="line" lang="diff"> seq_dict[hdr] = nt</span>
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239
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"> seq_len[hdr] = len(nt.replace("\n",""))</span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq_len_sort = sorted(seq_len.iteritems(), key=operator.itemgetter(1))</span></span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq_len_sort = sorted(iter(seq_len.items()), key=operator.itemgetter(1))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="242" 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">
242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"> seq_len_sort.reverse()</span>
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<td class="diff-line-num old old_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff"> ffo = open("%s"%(outputDir+os.sep+ref.split(os.sep)[-1]+".ref"),'w')</span>
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<td class="diff-line-num old old_line" data-linenumber="244" 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">
244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"> for item in seq_len_sort:</span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"><span class="p">@@ -750,7 +750,7 @@</span> if __name__ == "__main__":</span>
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<td class="diff-line-num old old_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"> if not inifile_exists:</span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"> if len(fnafiles) < 1 or ref == "":</span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff"> sys.stderr.write( "Parsnp requires 2 or more genomes to run, exiting\n")</span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print fnafiles, ref</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(fnafiles, ref)</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"> sys.exit(0)</span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff"> </span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff"> file_string = ""</span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff"><span class="p">@@ -779,7 +779,7 @@</span> if __name__ == "__main__":</span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"> run_command(command)</span>
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<td class="diff-line-num old old_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff"> mumif = open(outputDir+os.sep+"all.mumi",'r')</span>
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<td class="diff-line-num old old_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in mumif.xreadlines():</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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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in mumif:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"> line = line.replace("\n","")</span>
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<td class="diff-line-num old old_line" data-linenumber="261" 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">
261
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC261" class="line" lang="diff"> try:</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="17" 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="diff"> idx,mi = line.split(":")</span>
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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="17" 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="diff"><span class="p">@@ -791,13 +791,13 @@</span> if __name__ == "__main__":</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="diff"> i = 0</span>
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<td class="diff-line-num old old_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff"> for file in fnafiles:</span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff"> mumi_dict[i] = 1</span>
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<td class="diff-line-num old old_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " |->["+OK_GREEN+"OK"+ENDC+"]"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" |->["+OK_GREEN+"OK"+ENDC+"]")</span></span>
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<td class="diff-line-num old old_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"> finalfiles = []</span>
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<td class="diff-line-num old old_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"> lowest_mumi = 100</span>
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<td class="diff-line-num old old_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"> auto_ref = ""</span>
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<td class="diff-line-num old old_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"> if autopick_ref:</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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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for idx in mumi_dict.keys():</span></span>
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<td class="diff-line-num old old_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for idx in list(mumi_dict.keys()):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"> if mumi_dict[idx] < lowest_mumi:</span>
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<td class="diff-line-num old old_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"> auto_ref = seqdir+os.sep+fnafiles[idx]</span>
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<td class="diff-line-num old old_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"> ref = auto_ref </span>
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<td class="diff-line-num old old_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"><span class="p">@@ -813,9 +813,9 @@</span> if __name__ == "__main__":</span>
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<td class="diff-line-num old old_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff"> mumi_f = open(outputDir+os.sep+"recruited_genomes.lst",'w')</span>
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<td class="diff-line-num old old_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"> if VERBOSE:</span>
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<td class="diff-line-num old old_line" data-linenumber="283" 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">
283
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "RECRUITED GENOMES:\n"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="284" 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">
284
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("RECRUITED GENOMES:\n")</span></span>
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<td class="diff-line-num old old_line" data-linenumber="285" 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">
285
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC285" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sorted_x = sorted(mumi_dict.iteritems(), key=operator.itemgetter(1))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="287" 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">
287
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sorted_x = sorted(iter(mumi_dict.items()), key=operator.itemgetter(1))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="288" 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">
288
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC288" class="line" lang="diff"> scnt = 0</span>
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<td class="diff-line-num old old_line" data-linenumber="289" 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">
289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff"> mumivals = []</span>
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<td class="diff-line-num old old_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"> for item in sorted_x:</span>
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<td class="diff-line-num old old_line" data-linenumber="291" 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">
291
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC291" class="line" lang="diff"><span class="p">@@ -838,7 +838,7 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="292" 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">
292
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC292" class="line" lang="diff"> hpv = minv+(3*stdv)</span>
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<td class="diff-line-num old old_line" data-linenumber="293" 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">
293
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC293" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="294" 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">
294
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC294" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="295" 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">
295
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for idx in mumi_dict.keys():</span></span>
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<td class="diff-line-num old old_line" data-linenumber="296" 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">
296
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for idx in list(mumi_dict.keys()):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="297" 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">
297
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC297" class="line" lang="diff"> if mumi_dict[idx] < (float(mumidistance)) or curated:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="298" 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">
298
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC298" class="line" lang="diff"> if fastmum and mumi_dict[idx] > hpv:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="299" 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">
299
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC299" class="line" lang="diff"> continue</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="300" 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">
300
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC300" class="line" lang="diff"><span class="p">@@ -846,11 +846,11 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="301" 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">
301
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC301" class="line" lang="diff"> if mumi_only:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff"> mumi_f.write(os.path.abspath(seqdir+os.sep+fnafiles[idx])+",%f"%(mumi_dict[idx])+"\n")</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="303" 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">
303
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC303" class="line" lang="diff"> if VERBOSE:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="304" 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">
304
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t"+fnafiles[idx]</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="305" 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">
305
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t"+fnafiles[idx])</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="306" 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">
306
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC306" class="line" lang="diff"> finalfiles.append(fnafiles[idx])</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="307" 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">
307
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC307" class="line" lang="diff"> allfiles.append(fnafiles[idx])</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="308" 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">
308
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC308" class="line" lang="diff"> if VERBOSE:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="309" 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">
309
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print </span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="310" 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">
310
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print() </span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="311" 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">
311
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC311" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="312" 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">
312
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC312" class="line" lang="diff"> if curated:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="313" 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">
313
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC313" class="line" lang="diff"> for file in fnafiles:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="314" 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">
314
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC314" class="line" lang="diff"><span class="p">@@ -878,7 +878,7 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="315" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -883,7 +883,7 @@</span> if __name__ == "__main__":</span>
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315
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> continue</span>
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316
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> seq_dict[hdr] = nt</span>
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317
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> seq_len[hdr] = len(nt.replace("\n",""))</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="320" 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="23" 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">@@ -320,286 +23,3 @@ Last-Update: Fri, 13 Sep 2019 12:08:17 +0200</td>
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320
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> seq_len_sort.reverse()</span>
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321
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> ffo = open("%s"%(outputDir+os.sep+auto_ref.split(os.sep)[-1]+".ref"),'w')</span>
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322
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> for item in seq_len_sort:</span></pre>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="diff"><span class="p">@@ -888,8 +888,8 @@</span> if __name__ == "__main__":</span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"> ffo.close()</span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff"> auto_ref = outputDir+os.sep+auto_ref.split(os.sep)[-1]+".ref"</span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"> ref = auto_ref</span>
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<td class="diff-line-num old old_line" data-linenumber="327" 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">
327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print ref</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print ref</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print(ref)</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print(ref)</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="diff"> inifiled_closest = inifiled</span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"> if not inifile_exists:</span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff"> if len(finalfiles) < 1 or ref == "":</span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="diff"><span class="p">@@ -934,7 +934,7 @@</span> if __name__ == "__main__":</span>
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335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff"> </span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff"> </span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff"> #3)run parsnp (cores, grid?)</span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-->Running Parsnp multi-MUM search and libMUSCLE aligner.."</span></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-->Running Parsnp multi-MUM search and libMUSCLE aligner..")</span></span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="diff"> if not os.path.exists(outputDir+os.sep+"blocks"):</span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="diff"> os.mkdir(outputDir+os.sep+"blocks")</span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="diff"> command = ""</span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="diff"><span class="p">@@ -983,7 +983,7 @@</span> if __name__ == "__main__":</span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff"> totseqs = 0</span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="diff"> try:</span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff"> cf = open("%sparsnpAligner.log"%(outputDir+os.sep)) </span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in cf.xreadlines():</span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in cf:</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="diff"> if "Total coverage among all sequences:" in line:</span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"> coverage = line.split(":",1)[-1].replace("\n","")</span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="diff"> coverage = float(coverage.replace("%",""))/100.0</span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="diff"><span class="p">@@ -991,7 +991,7 @@</span> if __name__ == "__main__":</span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"> totlength += int(line.split(":",1)[-1].replace("\n","").split("bps")[0])</span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff"> totseqs +=1</span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="diff"> except IOError:</span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ERROR_RED+"parsnpAligner.log missing, parsnpAligner failed, exiting.."+ENDC</span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(ERROR_RED+"parsnpAligner.log missing, parsnpAligner failed, exiting.."+ENDC)</span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff"> sys.exit(1)</span>
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<td class="diff-line-num old old_line" data-linenumber="359" 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">
359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="diff"> </span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"> #update thresholds</span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="diff"><span class="p">@@ -1002,10 +1002,10 @@</span> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="362" 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">
362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"> sys.stderr.write( " |->["+WARNING_YELLOW+"WARNING"+ENDC+"]"+": aligned regions cover less than 10% of reference genome! please verify recruited genomes are all strain of interest"+ENDC)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="363" 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">
363
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC363" class="line" lang="diff"> else:</span>
</pre>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="diff"> pass</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " |->["+OK_GREEN+"OK"+ENDC+"]"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="366" 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">
366
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" |->["+OK_GREEN+"OK"+ENDC+"]")</span></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="diff"> t2 = time.time()</span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="diff"> elapsed = float(t2)-float(t1)</span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print "-->Getting list of LCBs.."</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print("-->Getting list of LCBs..")</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="diff"> allbfiles = glob.glob(outputDir+os.sep+"blocks/b*/*")</span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="diff"> blockfiles = []</span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="diff"> icnt = 0</span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="diff"><span class="p">@@ -1047,7 +1047,7 @@</span> if __name__ == "__main__":</span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="diff"> recombination_sites = {}</span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="diff"> bedfile = ""</span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="diff"> bedfile_dict = {}</span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-->Running PhiPack on LCBs to detect recombination.."</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-->Running PhiPack on LCBs to detect recombination..")</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="diff"> if run_recomb_filter and len(blockfiles) > 0:</span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="diff"> </span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="diff"> bedfile = open("%s/parsnp.rec"%(outputDir),'w')</span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="diff"><span class="p">@@ -1078,7 +1078,7 @@</span> if __name__ == "__main__":</span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="diff"> </span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="diff"> #run parallelPhiPack</span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="diff"> pool = Pool(processes=int(threads))</span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = pool.map_async(parallelPhiWrapper,tasks).get(sys.maxint)</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ result = pool.map_async(parallelPhiWrapper,tasks).get(sys.maxsize)</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="diff"> </span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="diff"> for i in result:</span>
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<td class="diff-line-num old old_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="diff"> if (i["status"] == 1):</span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="diff"><span class="p">@@ -1113,7 +1113,7 @@</span> if __name__ == "__main__":</span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="diff"> bedfile_dict[srpos] = "1\t%s\t%s\tREC\t%.3f\t+\n"%(srpos,pos+50+block_spos,eval)</span>
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<td class="diff-line-num old old_line" data-linenumber="394" 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">
394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="diff"> else:</span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="diff"> chrnum = 1</span>
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<td class="diff-line-num old old_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chr_spos = ref_seqs.keys()</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chr_spos = list(ref_seqs.keys())</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="diff"> for cs in chr_spos:</span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"> if block_spos < chr_spos:</span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="diff"> chrnum = ref_seqs[cs]</span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="diff"><span class="p">@@ -1129,7 +1129,7 @@</span> if __name__ == "__main__":</span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff"> </span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"> pool.close()</span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="diff"> pool.join()</span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- brkeys = bedfile_dict.keys()</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ brkeys = list(bedfile_dict.keys())</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="diff"> brkeys.sort()</span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="diff"> for key in brkeys:</span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="diff"> bedfile.write(bedfile_dict[key])</span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff"><span class="p">@@ -1160,14 +1160,14 @@</span> if __name__ == "__main__":</span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="diff"> run_command("harvesttools -q -i %s/parsnp.ggr -S "%(outputDir)+outputDir+os.sep+"parsnp.snps.mblocks")</span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="diff"> </span>
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413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="diff"> command = "fasttree -nt -quote -gamma -slow -boot 100 "+outputDir+os.sep+"parsnp.snps.mblocks > "+outputDir+os.sep+"parsnp.tree"</span>
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<td class="diff-line-num old old_line" data-linenumber="414" 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">
414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-->Reconstructing core genome phylogeny.."</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-->Reconstructing core genome phylogeny..")</span></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="diff"> run_command(command)</span>
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<td class="diff-line-num old old_line" data-linenumber="417" 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">
417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="diff"> #7)reroot to midpoint</span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="diff"> if os.path.exists("outtree"):</span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="diff"> os.system("rm outtree")</span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="diff"> </span>
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421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="diff"> if reroot_tree and len(finalfiles) > 1:</span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print "-->Midpoint reroot.."</span></span>
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423
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print("-->Midpoint reroot..")</span></span>
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424
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="diff"> try:</span>
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425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="diff"> mtree = open("%sparsnp.tree"%(outputDir+os.sep), 'r')</span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="diff"> mtreedata = mtree.read()</span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="diff"><span class="p">@@ -1175,32 +1175,32 @@</span> if __name__ == "__main__":</span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff"> tree = dendropy.Tree.get_from_string(mtreedata,"newick")</span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="diff"> tree.reroot_at_midpoint(update_splits=False)</span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="diff"> mftreef = tree.as_string('newick').split(" ",1)[1]</span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print mftreef</span></span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print(mftreef)</span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="diff"> mtreef = open(outputDir+os.sep+"parsnp.final.tree",'w')</span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="diff"> mtreef.write(mftreef)</span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="diff"> mtreef.close()</span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="diff"> os.system("mv %s %s"%(outputDir+os.sep+"parsnp.final.tree",outputDir+os.sep+"parsnp.tree"))</span>
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437
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="diff"> except IOError:</span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="diff"> sys.stderr.write( "ERROR: cannot process fasttree output, skipping midpoint reroot..\n")</span>
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439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " |->["+OK_GREEN+"OK"+ENDC+"]"</span></span>
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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" |->["+OK_GREEN+"OK"+ENDC+"]")</span></span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="diff"> </span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="diff"> </span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="diff"> if 1 or len(use_gingr) > 0:</span>
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444
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-->Creating Gingr input file.."</span></span>
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445
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-->Creating Gingr input file..")</span></span>
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446
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="diff"> if xtrafast or 1:</span>
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447
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="diff"> #if newick available, add</span>
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448
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="diff"> #new flag to update branch lengths</span>
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449
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="diff"> run_command("harvesttools --midpoint-reroot -u -q -i "+outputDir+os.sep+"parsnp.ggr -o "+outputDir+os.sep+"parsnp.ggr -n %s"%(outputDir+os.sep+"parsnp.tree "))</span>
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450
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="diff"> </span>
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451
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " |->["+OK_GREEN+"OK"+ENDC+"]"</span></span>
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452
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" |->["+OK_GREEN+"OK"+ENDC+"]")</span></span>
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<td class="diff-line-num old old_line" data-linenumber="453" 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">
453
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="diff"> </span>
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454
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-->Calculating wall clock time.. "</span></span>
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455
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-->Calculating wall clock time.. ")</span></span>
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456
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="diff"> if float(elapsed)/float(60.0) > 60:</span>
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457
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " |->"+BOLDME+"Aligned %d genomes in %.2f hours"%(totseqs,float(elapsed)/float(3600.0))+ENDC</span></span>
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458
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" |->"+BOLDME+"Aligned %d genomes in %.2f hours"%(totseqs,float(elapsed)/float(3600.0))+ENDC)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="459" 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">
459
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="diff"> elif float(elapsed) > 60:</span>
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<td class="diff-line-num old old_line" data-linenumber="460" 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">
460
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " |->"+BOLDME+"Aligned %d genomes in %.2f minutes"%(totseqs,float(elapsed)/float(60.0))+ENDC</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="461" 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">
461
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" |->"+BOLDME+"Aligned %d genomes in %.2f minutes"%(totseqs,float(elapsed)/float(60.0))+ENDC)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="462" 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">
462
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="diff"> else: </span>
</pre>
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463
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC463" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " |->"+BOLDME+"Aligned %d genomes in %.2f seconds"%(totseqs,float(elapsed))+ENDC</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="464" 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">
464
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" |->"+BOLDME+"Aligned %d genomes in %.2f seconds"%(totseqs,float(elapsed))+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="465" 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">
465
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="diff"> #cleanup</span>
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466
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="diff"> rmfiles = glob.glob(outputDir+os.sep+"*.aln")</span>
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<td class="diff-line-num old old_line" data-linenumber="467" 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">
467
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="diff"> #rmfiles2 = glob.glob(outputDir+os.sep+"blocks/b*/*")</span>
</pre>
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468
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC468" class="line" lang="diff"><span class="p">@@ -1211,33 +1211,33 @@</span> if __name__ == "__main__":</span>
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469
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC469" class="line" lang="diff"> os.system("rm -rf %s"%(file))</span>
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470
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC470" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="471" 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">
471
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC471" class="line" lang="diff"> filepres = 0</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="472" 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">
472
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC472" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print BOLDME+"\n<<Parsnp finished! All output available in %s>>"%(outputDir)+ENDC</span></span>
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<td class="diff-line-num old old_line" data-linenumber="473" 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">
473
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC473" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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<td class="diff-line-num old old_line" data-linenumber="474" 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">
474
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print BOLDME+"Validating output directory contents..."+ENDC</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="475" 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">
475
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC475" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print BOLDME+"\t1)parsnp.tree:\t\tnewick format tree"+ENDC,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="476" 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">
476
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(BOLDME+"\n<<Parsnp finished! All output available in %s>>"%(outputDir)+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="477" 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">
477
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC477" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="478" 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">
478
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(BOLDME+"Validating output directory contents..."+ENDC)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="479" 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">
479
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<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(BOLDME+"\t1)parsnp.tree:\t\tnewick format tree"+ENDC, end=' ')</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="480" 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">
480
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC480" class="line" lang="diff"> if os.path.exists("%sparsnp.tree"%(outputDir+os.sep)) and os.path.getsize("%sparsnp.tree"%(outputDir+os.sep)) > 0:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="481" 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">
481
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<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t\t\t["+OK_GREEN+"OK"+ENDC+"]"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="482" 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">
482
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<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\t["+OK_GREEN+"OK"+ENDC+"]")</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="483" 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">
483
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC483" class="line" lang="diff"> filepres+=1</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="484" 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">
484
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC484" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="485" 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">
485
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC485" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t|->"+ERROR_RED+"MISSING"+ENDC</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="486" 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">
486
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC486" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print BOLDME+"\t2)parsnp.ggr:\t\tharvest input file for gingr (GUI)"+ENDC,</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="487" 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">
487
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC487" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t|->"+ERROR_RED+"MISSING"+ENDC)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="488" 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">
488
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(BOLDME+"\t2)parsnp.ggr:\t\tharvest input file for gingr (GUI)"+ENDC, end=' ')</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="489" 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">
489
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC489" class="line" lang="diff"> if os.path.exists("%sparsnp.ggr"%(outputDir+os.sep)) and os.path.getsize("%sparsnp.ggr"%(outputDir+os.sep)) > 0:</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="490" 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">
490
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t["+OK_GREEN+"OK"+ENDC+"]"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="491" 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">
491
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t["+OK_GREEN+"OK"+ENDC+"]")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="492" 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">
492
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC492" class="line" lang="diff"> filepres+=1</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="493" 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">
493
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC493" class="line" lang="diff"> else:</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="494" 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">
494
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC494" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t|->"+ERROR_RED+"MISSING"+ENDC</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="495" 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">
495
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC495" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print BOLDME+"\t3)parsnp.xmfa:\t\tXMFA formatted multi-alignment"+ENDC,</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="496" 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">
496
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC496" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t|->"+ERROR_RED+"MISSING"+ENDC)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="497" 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">
497
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(BOLDME+"\t3)parsnp.xmfa:\t\tXMFA formatted multi-alignment"+ENDC, end=' ')</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="498" 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">
498
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC498" class="line" lang="diff"> if os.path.exists("%sparsnp.xmfa"%(outputDir+os.sep)) and os.path.getsize("%sparsnp.xmfa"%(outputDir+os.sep)) > 0:</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="499" 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">
499
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC499" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t\t["+OK_GREEN+"OK"+ENDC+"]"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="500" 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">
500
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC500" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t["+OK_GREEN+"OK"+ENDC+"]")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="501" 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">
501
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC501" class="line" lang="diff"> filepres+=1</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="502" 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">
502
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC502" class="line" lang="diff"> else:</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="503" 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">
503
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC503" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t|->"+ERROR_RED+"MISSING"+ENDC</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="504" 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">
504
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC504" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t|->"+ERROR_RED+"MISSING"+ENDC)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="505" 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">
505
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC505" class="line" lang="diff"> if filepres == 3:</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="506" 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">
506
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC506" class="line" lang="diff"> pass</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="507" 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">
507
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC507" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="508" 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">
508
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC508" class="line" lang="diff"> else:</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="509" 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">
509
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC509" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t\t["+ERROR_RED+"Output files missing, something went wrong. Check logs and relaunch or contact developers for assistance"+ENDC+"]"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="510" 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">
510
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="511" 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">
511
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t["+ERROR_RED+"Output files missing, something went wrong. Check logs and relaunch or contact developers for assistance"+ENDC+"]")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="512" 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">
512
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC512" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="513" 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">
513
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC513" class="line" lang="diff"> if os.path.exists("%sblocks"%(outputDir+os.sep)):</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="514" 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">
514
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC514" class="line" lang="diff"> os.rmdir("%sblocks"%(outputDir+os.sep))</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="515" 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">
515
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC515" class="line" lang="diff"> if os.path.exists("allmums.out"):</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="516" 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">
516
</td>
<td class="diff-line-num new_line old" data-linenumber="26" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC516" class="line" lang="diff"><span class="p">@@ -1281,6 +1281,6 @@</span> if __name__ == "__main__":</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="517" 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">
517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="diff"> #check if available first</span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="diff"> rc = 0</span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="diff"> if binary_type == "osx":</span>
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520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ">>Launching gingr.."</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(">>Launching gingr..")</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="diff"> os.system("open -n %s --args %s/parsnp.ggr"%(use_gingr,outputDir))</span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="diff"> </span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/install.py</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/install.py</span></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="diff"><span class="p">@@ -1,12 +1,12 @@</span></span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="diff"> import os,sys,string</span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="diff"> #parsnp basic INSTALL script</span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="diff"> user_home = os.environ["HOME"]</span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print "<<Welcome to Parsnp utility script install>>"</span></span>
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531
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("<<Welcome to Parsnp utility script install>>")</span></span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="diff"> </span>
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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="diff"> #check for python version</span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="diff"> if (sys.version_info[0] < 2) or (sys.version_info[0] == 2 and sys.version_info[1] < 6):</span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="diff"> </span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Python version is %s. Parsnp requires at least 2.6"%(sys.version)</span></span>
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537
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Python version is %s. Parsnp requires at least 2.6"%(sys.version))</span></span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="diff"> sys.exit(1)</span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="diff"> </span>
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540
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="diff"> #complete shebang</span>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/script/shuffle.py</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/script/shuffle.py</span></span>
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543
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span> if __name__ == "__main__":</span>
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544
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="diff"> rnumber = 0</span>
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545
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="diff"> shuffleperseq = 1</span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="diff"> if len(sys.argv) < 6:</span>
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547
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\nUsage: shuffleGenome <FastA input file> <output file> <Rearrangement size> <Number of rearrangements> <Shuffled sequences per seq>"</span></span>
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548
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\nUsage: shuffleGenome <FastA input file> <output file> <Rearrangement size> <Number of rearrangements> <Shuffled sequences per seq>")</span></span>
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549
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="diff"> sys.exit(1)</span>
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550
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="diff"> else:</span>
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551
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="diff"> infileName = sys.argv[1]</span>
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552
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="diff"><span class="p">@@ -77,22 +77,22 @@</span> if __name__ == "__main__":</span>
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553
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="diff"> header = infile.readline()</span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="diff"> infiled = infile.read()</span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="diff"> filelen = len(infiled)</span>
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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\nInput sequence:%s"%seqfile</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Input sequence length: %d\n"%filelen</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\nInput sequence:%s"%seqfile)</span></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Input sequence length: %d\n"%filelen)</span></span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="diff"> </span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="diff"> #split genome into filelen/rsize parts</span>
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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="diff"> partlist = []</span>
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563
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="diff"> pos = 0</span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="diff"> if rsize > filelen:</span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="diff"> rsize = filelen</span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for part in xrange(0,filelen/rsize):</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for part in range(0,filelen/rsize):</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="diff"> partlist.append(infiled[pos:(part+1)*rsize])</span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="diff"> pos +=rsize</span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="diff"> </span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="diff"> partlist.append(infiled[pos:])</span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="diff"> </span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="diff"> </span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for shuffleit in xrange(0,shuffleperseq): </span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for shuffleit in range(0,shuffleperseq): </span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="diff"> count = 0</span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="diff"> seq = ""</span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="diff"> parttemp = ""</span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="diff"><span class="p">@@ -114,13 +114,13 @@</span> if __name__ == "__main__":</span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="diff"> parttemp = partlist[part1]</span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="diff"> partlist[part1] = partlist[part2]</span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="diff"> partlist[part2] = parttemp</span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Transposition"</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " Positions %d and %d swapped"%(part1,part2)</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Transposition")</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" Positions %d and %d swapped"%(part1,part2))</span></span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="diff"> elif operation == 2:</span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="diff"> #inversion</span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="diff"> partlist[part1] = invertSeq(partlist[part1])</span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Inversion"</span></span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " Position %d"%part1</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Inversion")</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" Position %d"%part1)</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="diff"> </span>
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595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="diff"> </span>
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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="diff"> </span>
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597
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="diff"><span class="p">@@ -137,7 +137,7 @@</span> if __name__ == "__main__":</span>
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598
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="diff"> #write output to file</span>
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599
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="diff"> fname = seqfile[:-4]</span>
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600
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="diff"> fname+= "_Shuffled_%d.fna"%(shuffleit+1)</span>
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601
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "output: %s"%(fname)</span></span>
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602
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("output: %s"%(fname))</span></span>
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603
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="diff"> </span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="diff"> fout = open(fname,'w')</span>
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605
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="diff"> fout.write(output)</span></pre>
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<li id="82bdf410ee3abb85c057e0147f43e488d2f00daf">
<a href="https://salsa.debian.org/med-team/parsnp/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#82bdf410ee3abb85c057e0147f43e488d2f00daf"><strong>debian/patches/proper_calls_to_tools.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" 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">@@ -49,7 +49,7 @@ Description: Fix path to Debian installed tools</td>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> #set MUMmer paths</span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> if os.path.exists("%s/MUMmer/nucmer_run"%(PARSNP_DIR)):</span>
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51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> ff = open("%s/MUMmer/nucmer_run"%(PARSNP_DIR))</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="p">@@ -78<span class="idiff left right">4,12 +770</span>,12 @@</span> if __name__ == "__main__":</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -78<span class="idiff left right">9,12 +775</span>,12 @@</span> if __name__ == "__main__":</span>
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53
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> if use_parsnp_mumi and not curated:</span>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> sys.stderr.write( "-->Calculating MUMi..\n")</span>
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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> if not inifile_exists:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="64" 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="64" 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">@@ -64,7 +64,7 @@ Description: Fix path to Debian installed tools</td>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> run_command(command)</span>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> try:</span>
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66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> mumif = open(outputDir+os.sep+"all.mumi",'r')</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="p">@@ -96<span class="idiff left right">2,14 +948</span>,14 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -96<span class="idiff left right">7,14 +953</span>,14 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> if command == "" and xtrafast and 0:</span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> command = "%s/parsnpA_fast %sparsnpAligner.ini"%(PARSNP_DIR,outputDir+os.sep)</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> elif command == "":</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">@@ -82,7 +82,7 @@ Description: Fix path to Debian installed tools</td>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> run_command(command)</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left right">59,21 +1145</span>,21 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left right">64,21 +1150</span>,21 @@</span> if __name__ == "__main__":</span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> if xtrafast or 1:</span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> #add genbank here, if present</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> if len(genbank_ref) != 0:</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">@@ -107,15 +107,15 @@ Description: Fix path to Debian installed tools</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> </span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "%s/ft -nt -quote -gamma -slow -boot 100 "%(PARSNP_DIR)+outputDir+os.sep+"parsnp.snps.mblocks > "+outputDir+os.sep+"parsnp.tree"</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "fasttree -nt -quote -gamma -slow -boot 100 "+outputDir+os.sep+"parsnp.snps.mblocks > "+outputDir+os.sep+"parsnp.tree"</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"> print<span class="idiff left right"> "-->Reconstructing core genome phylogeny.."</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> print<span class="idiff left right">("-->Reconstructing core genome phylogeny..")</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"> run_command(command)</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"> #7)reroot to midpoint</span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="p">@@ -120<span class="idiff left right">4,7 +1190</span>,7 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="p">@@ -120<span class="idiff left right">9,7 +1195</span>,7 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"> if xtrafast or 1:</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> #if newick available, add</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> #new flag to update branch lengths</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_command("%s/harvest --midpoint-reroot -u -q -i "%(PARSNP_DIR)+outputDir+os.sep+"parsnp.ggr -o "+outputDir+os.sep+"parsnp.ggr -n %s"%(outputDir+os.sep+"parsnp.tree "))</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_command("harvesttools --midpoint-reroot -u -q -i "+outputDir+os.sep+"parsnp.ggr -o "+outputDir+os.sep+"parsnp.ggr -n %s"%(outputDir+os.sep+"parsnp.tree "))</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"> print<span class="idiff left right"> " |->["+OK_GREEN+"OK"+ENDC+"]"</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> print<span class="idiff left right">(" |->["+OK_GREEN+"OK"+ENDC+"]")</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#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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<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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<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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<li id="2e8ce15c0b817fa44897094ab9c5f2c504a96ccd">
<a href="https://salsa.debian.org/med-team/parsnp/compare/e25203ae06920c733af26b91acda6ea6230f402a...87af9db0b3b158ad7e42635f52a1e138cf988260#2e8ce15c0b817fa44897094ab9c5f2c504a96ccd"><strong>script/shuffle.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="51" 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">@@ -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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<td class="diff-line-num old old_line" data-linenumber="54" 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="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="diff-line-num unfold js-unfold new_line" data-linenumber="77" 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">@@ -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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<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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<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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<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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<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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<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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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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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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<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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<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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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> </span>
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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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