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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/scoary">Debian Med / scoary</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/scoary/commit/b28bfa5446c06b4011c9d73f103cd8b83ca7dcc3">b28bfa54</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T14:14:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scoary/commit/e38abeea286e69bee5042c4be6fd25c3eaeaf099">e38abeea</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T14:16:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust packaging to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scoary/commit/370f6dc36c1e6c290c65911847470542b75b507f">370f6dc3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T14:16:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scoary/commit/f635c072de0321d257461571177818af056c4822">f635c072</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T14:16:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
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−
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
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+
debian/patches/2to3.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/scoary/compare/902691ea72f00079155953988bae8a0b3103aa0f...f635c072de0321d257461571177818af056c4822#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">scoary (1.6.16-2) UNRELEASED; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #938447</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 13 Sep 2019 16:13:39 +0200</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">scoary (1.6.16-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Initial release (Closes: #920857)</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/scoary/compare/902691ea72f00079155953988bae8a0b3103aa0f...f635c072de0321d257461571177818af056c4822#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">9</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/scoary/compare/902691ea72f00079155953988bae8a0b3103aa0f...f635c072de0321d257461571177818af056c4822#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,14 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>=9</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python-all,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-setuptools,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python-scipy (>= 0.16),</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># Test-Depends:</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python-nose</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-scipy (>= 0.16),</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-nose <!nocheck></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.0</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/scoary</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/scoary.git</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://github.com/AdmiralenOla/Scoary</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,8 +17,9 @@ Homepage: https://github.com/AdmiralenOla/Scoary</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Package: scoary</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> python-pkg-resources</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3-pkg-resources,</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> python3-scipy</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Suggests: roary</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: pangenome-wide association studies</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Scoary is designed to take the gene_presence_absence.csv file from</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/scoary/compare/902691ea72f00079155953988bae8a0b3103aa0f...f635c072de0321d257461571177818af056c4822#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/938447</span></span>
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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Fri, 13 Sep 2019 16:13:39 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/scoary.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scoary.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></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;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> # Scoary - Microbial Pan-GWAS. Associates genes in Roary output with phenotypes</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # Copyright (C) 2016 Ola Brynildsrud (ola.brynildsrud@fhi.no)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scoary/GUI.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scoary/GUI.py</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span> import sys, os</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> import threading</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> try:</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import Tkinter</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import tkinter</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> except ImportError:</span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> #Python 3 issues</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span> except ImportError:</span>
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<td class="diff-line-num new new_line" data-linenumber="32" 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">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> sys.exit("Need to have Tkinter / tkinter installed")</span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> try:</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import tkFileDialog</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import tkinter.filedialog</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> except ImportError:</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> # Python 3 issues</span>
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="40" 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">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -31,7 +31,7 @@</span> except ImportError:</span>
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<td class="diff-line-num new new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> sys.exit("Could not find tkFileDialog / filedialog")</span>
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<td class="diff-line-num new new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import ttk</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" 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">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import tkinter.ttk</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> except ImportError:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> # Python 3 issues</span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -63,12 +63,12 @@</span> except ImportError:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="50" 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">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> from pkg_resources import resource_string, resource_filename</span>
</pre>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class ScoaryGUI(Tkinter.Tk):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class ScoaryGUI(tkinter.Tk):</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> Create the main GUI window</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> def __init__(self,parent):</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Tk.__init__(self,parent)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Tk.__init__(self,parent)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> self.parent = parent</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> self.Scoary_parameters = {"GPA": None,"Trait":None,"Tree":None,</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -86,15 +86,15 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> self.initialize_menu()</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.toppart = Tkinter.Frame(self,height="350",width="800")</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.bottompart = Tkinter.Frame(self,height="50",width="800")</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.toppart = tkinter.Frame(self,height="350",width="800")</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.bottompart = tkinter.Frame(self,height="50",width="800")</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> self.toppart.pack(side='top',expand=False)</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> self.bottompart.pack(side='bottom',expand=True,fill='both')</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.nwpart = Tkinter.Frame(self.toppart,</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.nwpart = tkinter.Frame(self.toppart,</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> height="350",</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> width="250")</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.nepart = Tkinter.LabelFrame(self.toppart,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.nepart = tkinter.LabelFrame(self.toppart,</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> height="350",</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> width="550",</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> text="Control panel")</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="p">@@ -103,7 +103,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> # Add further frames to top or bottom</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.logocanvas = Tkinter.Canvas(self.nwpart,</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.logocanvas = tkinter.Canvas(self.nwpart,</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> height="250",</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> width="250",</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> relief="ridge",</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="p">@@ -111,7 +111,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> highlightthickness=0)</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> self.logocanvas.pack(side='top',expand=False)</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.citationframe = Tkinter.Frame(self.nwpart,</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.citationframe = tkinter.Frame(self.nwpart,</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> height="100",</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> width="250")</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> self.citationframe.pack(side='bottom',expand=False,fill='none')</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="p">@@ -127,15 +127,15 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> Initialize the menu at the top</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.menubar = Tkinter.Menu(self,relief="flat")</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- filemenu = Tkinter.Menu(self.menubar,tearoff=0)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.menubar = tkinter.Menu(self,relief="flat")</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;">+ filemenu = tkinter.Menu(self.menubar,tearoff=0)</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> filemenu.add_command(label="About",command=self.AboutScoary)</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> filemenu.add_separator()</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> filemenu.add_command(label="Quit",command=self.quit)</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> self.filemenu = filemenu</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> self.menubar.add_cascade(label="File",menu=self.filemenu)</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optsmenu = Tkinter.Menu(self.menubar,tearoff=0)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optsmenu = tkinter.Menu(self.menubar,tearoff=0)</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> optsmenu.add_command(label="Clear", command=self.ClearAll)</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> optsmenu.add_command(label="Test example",</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> command=self.TestExample)</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -149,7 +149,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> Initialize the citation frame - below the logo</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> myfontstyle = ("Arial",8)</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.citation = Tkinter.Label(self.citationframe,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.citation = tkinter.Label(self.citationframe,</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> text=self.citationtext(),</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> anchor='center',</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> justify='center',</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="p">@@ -162,13 +162,13 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> """</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> frame = self.bottompart</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- frame.pb = ttk.Progressbar(frame,</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ frame.pb = tkinter.ttk.Progressbar(frame,</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> orient='horizontal',</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> mode='determinate',</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> maximum=100)</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> frame.pb.pack(fill='both',expand=True,side='top')</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 class="gd" style="color: #000; background-color: #fdd;">- frame.lab = Tkinter.Label(frame,text=u"Awaiting input options")</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ frame.lab = tkinter.Label(frame,text="Awaiting input options")</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> frame.lab.pack(in_=frame.pb,expand=True)</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> #sys.stdout = StdoutToLabel(frame.lab, progressbar=frame.pb)</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> sys.stdout = StdoutToLabel(frame.lab,</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="p">@@ -181,87 +181,87 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> board = self.nepart</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.GPAentryVariable = Tkinter.StringVar()</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.GPAentryVariable = tkinter.StringVar()</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> board.GPAentry = \</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Entry(board, </span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(board, </span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> textvariable = self.GPAentryVariable,</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> width=60)</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> board.GPAentry.grid(column=0,row=0,sticky='W',columnspan=2)</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> self.GPAentryVariable.set("Path to gene presence absence file")</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.TraitsentryVariable = Tkinter.StringVar()</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.TraitsentryVariable = tkinter.StringVar()</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> board.Traitsentry = \</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;">- Tkinter.Entry(board, </span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(board, </span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> textvariable=self.TraitsentryVariable,</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> width=60)</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> board.Traitsentry.grid(column=0,row=1,sticky='W',columnspan=2)</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> self.TraitsentryVariable.set("Path to traits/phenotype file")</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> </span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.TreeentryVariable = Tkinter.StringVar()</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.TreeentryVariable = tkinter.StringVar()</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> board.Treeentry = \</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Entry(board, </span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(board, </span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> textvariable=self.TreeentryVariable,</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> width=60)</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> board.Treeentry.grid(column=0,row=2,sticky='W',columnspan=2)</span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> self.TreeentryVariable.set(</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> "(Optional) Path to custom tree file")</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> </span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.RestrictVariable = Tkinter.StringVar()</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.RestrictVariable = tkinter.StringVar()</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> board.Restrictentry = \</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Entry(board, </span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(board, </span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> textvariable=self.RestrictVariable,</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> width=60)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> board.Restrictentry.grid(column=0,row=3,sticky='W',columnspan=2)</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> self.RestrictVariable.set(</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> "(Optional) Path to file naming isolates to include")</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> </span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.Outputdir = Tkinter.StringVar()</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.Outputdir = tkinter.StringVar()</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> board.Outputentry = \</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Entry(board, </span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(board, </span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> textvariable=self.Outputdir,</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> width=60)</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> board.Outputentry.grid(column=0,row=4,sticky='W',columnspan=2)</span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> self.Outputdir.set("(Optional) Output directory")</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> </span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> browsebuttonGPA = \</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Button(board, </span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Browse...", </span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Button(board, </span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Browse...", </span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> command=self.BrowseButtonClickGPA)</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> browsebuttonGPA.grid(column=2,row=0,sticky='e')</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> </span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> browsebuttonTraits = \</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Button(board,</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Browse...", </span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Button(board,</span></span>
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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;">+ text="Browse...", </span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> command=self.BrowseButtonClickTraits)</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> browsebuttonTraits.grid(column=2,row=1,sticky='e')</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> browsebuttonTreeFile = \</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Button(board,</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Browse...", </span></span>
</pre>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Button(board,</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Browse...", </span></span>
</pre>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> command=self.BrowseButtonClickTreeFile)</span>
</pre>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> browsebuttonTreeFile.grid(column=2,row=2,sticky='e')</span>
</pre>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
</pre>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> browsebuttonRestrict = \</span>
</pre>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Button(board,</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Browse...",</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Button(board,</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Browse...",</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> command=self.BrowseButtonClickRestrict)</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> browsebuttonRestrict.grid(column=2,row=3,sticky='e')</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> browsebuttonOutput = \</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Button(board,</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Browse...",</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Button(board,</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Browse...",</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> command=self.BrowseButtonClickOutput)</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> browsebuttonOutput.grid(column=2,row=4,sticky='e')</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> # Initialize frame for cutoffs</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- board.pframe = Tkinter.LabelFrame(board,</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ board.pframe = tkinter.LabelFrame(board,</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> text="Cut-offs",</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> relief='ridge')</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> board.pframe.grid(column=0,row=5,sticky='w')</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> self.initialize_pvalueframe()</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> # Initialize frame for misc options</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- board.miscframe = Tkinter.LabelFrame(board,</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ board.miscframe = tkinter.LabelFrame(board,</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> text="Misc options",</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> relief='ridge')</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> board.miscframe.grid(column=1,row=5,sticky='e',columnspan=2)</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="p">@@ -269,26 +269,26 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> </span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> ## Create extra space</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- board.emptyspace = Tkinter.Frame(board)</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ board.emptyspace = tkinter.Frame(board)</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> board.emptyspace.grid(column=0,row=6,columnspan=3,pady=(20,20))</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> masterbuttonfont = ("Courier", 16)</span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RunButton = Tkinter.Button(board.emptyspace,</span></span>
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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;">- text=u"Run analysis",</span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RunButton = tkinter.Button(board.emptyspace,</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Run analysis",</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> font=masterbuttonfont,</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> command=self.RunAnalysis,</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> padx=15,pady=10)</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> RunButton.grid(column=2,row=0)</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> </span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- QuitButton = Tkinter.Button(board.emptyspace,</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Quit",</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ QuitButton = tkinter.Button(board.emptyspace,</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Quit",</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> font=masterbuttonfont,</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> command=self.quit,padx=15,pady=10)</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> QuitButton.grid(column=1,row=0)</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> </span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- HelpButton = Tkinter.Button(board.emptyspace,</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Help",</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ HelpButton = tkinter.Button(board.emptyspace,</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Help",</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> font=masterbuttonfont,</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> command=self.HelpButton,</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> padx=15,pady=10)</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="p">@@ -302,100 +302,100 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> miscframe = board.miscframe</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> # Max hits</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.mhtext = Tkinter.StringVar()</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- miscframe.mhlab = Tkinter.Label(miscframe,</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.mhtext = tkinter.StringVar()</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ miscframe.mhlab = tkinter.Label(miscframe,</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> textvariable=self.mhtext)</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> miscframe.mhlab.grid(column=0,row=0,sticky='w')</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> self.mhtext.set("Max hits")</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> </span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.maxhitsvar = Tkinter.StringVar()</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.maxhitsvar = tkinter.StringVar()</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> miscframe.maxhitsentry = \</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Entry(miscframe,</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(miscframe,</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> textvariable=self.maxhitsvar,</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> width=8)</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> miscframe.maxhitsentry.grid(column=1,row=0)</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> self.maxhitsvar.set("")</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> </span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> # Delimiter</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.delimtext = Tkinter.StringVar()</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.delimtext = tkinter.StringVar()</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> miscframe.delim = \</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Label(miscframe,</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Label(miscframe,</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> textvariable=self.delimtext)</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> miscframe.delim.grid(column=0,row=1,sticky='w')</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> self.delimtext.set("Delimiter")</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.delimvar = Tkinter.StringVar()</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.delimvar = tkinter.StringVar()</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> miscframe.delimentry = \</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Entry(miscframe,</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(miscframe,</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> textvariable=self.delimvar,</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> width=8)</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> miscframe.delimentry.grid(column=1,row=1)</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> self.delimvar.set(",")</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> </span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> # Starting column</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.sctext = Tkinter.StringVar()</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.sctext = tkinter.StringVar()</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> miscframe.sclab = \</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Label(miscframe,</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Label(miscframe,</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> textvariable=self.sctext)</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> miscframe.sclab.grid(row=2,column=0,sticky='w')</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> self.sctext.set("Startcol GPA file")</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> </span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.scvar = Tkinter.StringVar()</span></span>
</pre>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- miscframe.sc = Tkinter.Entry(miscframe,textvariable=self.scvar,width=8)</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.scvar = tkinter.StringVar()</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ miscframe.sc = tkinter.Entry(miscframe,textvariable=self.scvar,width=8)</span></span>
</pre>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> miscframe.sc.grid(row=2,column=1)</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> self.scvar.set("15")</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> </span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> # Permutations</span>
</pre>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.permtext = Tkinter.StringVar()</span></span>
</pre>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.permtext = tkinter.StringVar()</span></span>
</pre>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> miscframe.permlab = \</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Label(miscframe,</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Label(miscframe,</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> textvariable=self.permtext)</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> miscframe.permlab.grid(row=3,column=0,sticky='w')</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> self.permtext.set("Permutations")</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> </span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.permvar = Tkinter.StringVar()</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.permvar = tkinter.StringVar()</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> miscframe.perm = \</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Entry(miscframe,</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Entry(miscframe,</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> textvariable=self.permvar,</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> width=8)</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> miscframe.perm.grid(row=3,column=1)</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> self.permvar.set("0")</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> </span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> # No timestamp</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.notimevar = Tkinter.IntVar()</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.notimevar = tkinter.IntVar()</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> miscframe.notime = \</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(miscframe,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="374" 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">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"No timestamp",</span></span>
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<td class="diff-line-num new new_line" data-linenumber="375" 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">
375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(miscframe,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="376" 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">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="No timestamp",</span></span>
</pre>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> onvalue=1,</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> offvalue=0,</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> variable=self.notimevar)</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> miscframe.notime.grid(row=5,column=0,sticky='w')</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"> # Write tree</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.writetreevar = Tkinter.IntVar()</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.writetreevar = tkinter.IntVar()</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> miscframe.writetree = \</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(miscframe,</span></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;">- text=u"Write tree",</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;">+ tkinter.Checkbutton(miscframe,</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Write tree",</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> onvalue=1,</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> offvalue=0,</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> variable=self.writetreevar)</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> miscframe.writetree.grid(row=6,column=0,sticky='w')</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> </span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> # No_pairwise</span>
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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;">- self.nopairwisevar = Tkinter.IntVar()</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;">+ self.nopairwisevar = tkinter.IntVar()</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> miscframe.nopairwise = \</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(miscframe,</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"No pairwise",</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(miscframe,</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="No pairwise",</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> onvalue=1,</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> offvalue=0,</span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> variable=self.nopairwisevar)</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> miscframe.nopairwise.grid(row=7,column=0,sticky='w')</span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> # Collapse</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.collapsevar = Tkinter.IntVar()</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.collapsevar = tkinter.IntVar()</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> miscframe.collapse = \</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(miscframe,</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Collapse corr",</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(miscframe,</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;">+ text="Collapse corr",</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> onvalue=1,</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> offvalue=0,</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> variable=self.collapsevar)</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="p">@@ -410,59 +410,59 @@</span> class ScoaryGUI(Tkinter.Tk):</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"> # Add p-value checkboxes</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> </span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.naivetext = Tkinter.StringVar()</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pVar = Tkinter.IntVar()</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.naivetext = tkinter.StringVar()</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pVar = tkinter.IntVar()</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> self.pVar.set(1)</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pBVar = Tkinter.IntVar()</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pBHVar = Tkinter.IntVar()</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pstext = Tkinter.StringVar()</span></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;">- self.pPWVar = Tkinter.IntVar()</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pEPWVar = Tkinter.IntVar()</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pBVar = tkinter.IntVar()</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pBHVar = tkinter.IntVar()</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pstext = tkinter.StringVar()</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pPWVar = tkinter.IntVar()</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pEPWVar = tkinter.IntVar()</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> self.pEPWVar.set(1)</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;">- self.pPermVar = Tkinter.IntVar()</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;">+ self.pPermVar = tkinter.IntVar()</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"> pframe.naivelab = \</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Label(pframe,</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Label(pframe,</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"> textvariable=self.naivetext)</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.naivetext.set(u"Pop structure-naive filters")</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.naivetext.set("Pop structure-naive filters")</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> pframe.pNcheck = \</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(pframe,</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Naive (Fisher's)",</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(pframe,</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;">+ text="Naive (Fisher's)",</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> onvalue=1,</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> offvalue=0,</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"> variable=self.pVar)</span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> pframe.pBcheck = \</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;">- Tkinter.Checkbutton(pframe,</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Bonferroni",</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(pframe,</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Bonferroni",</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> onvalue=1,</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> offvalue=0,</span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> variable=self.pBVar)</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> pframe.pBHcheck = \</span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> pframe,</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Benjamini-Hochberg",</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Benjamini-Hochberg",</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> onvalue=1,</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> offvalue=0,</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> variable=self.pBHVar)</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> pframe.pslab = \</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Label(pframe,</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Label(pframe,</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> textvariable=self.pstext)</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pstext.set(u"Pop structure-aware filters")</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pstext.set("Pop structure-aware filters")</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> pframe.pPWcheck = \</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(pframe,</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Pairwise comparison (Best)",</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(pframe,</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Pairwise comparison (Best)",</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> onvalue=1,</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> offvalue=0,</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> variable=self.pPWVar)</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> pframe.pEPWcheck = \</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(pframe,</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Pairwise comparison (Entire)",</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(pframe,</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Pairwise comparison (Entire)",</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> onvalue=1,</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> offvalue=0,</span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> variable=self.pEPWVar)</span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> pframe.pPermcheck = \</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Checkbutton(pframe,</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- text=u"Empirical p-value (Permutation)",</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Checkbutton(pframe,</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ text="Empirical p-value (Permutation)",</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> onvalue=1,</span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> variable=self.pPermVar)</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="p">@@ -478,29 +478,29 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> </span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> # Add p-value entry cells</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> </span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pNaive = Tkinter.StringVar()</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pBonf = Tkinter.StringVar()</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pBH = Tkinter.StringVar()</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pPW = Tkinter.StringVar()</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pEPW = Tkinter.StringVar()</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.pPerm = Tkinter.StringVar()</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pNaive = tkinter.StringVar()</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pBonf = tkinter.StringVar()</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pBH = tkinter.StringVar()</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pPW = tkinter.StringVar()</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pEPW = tkinter.StringVar()</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.pPerm = tkinter.StringVar()</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> </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;">- pframe.pNaiveEntry = Tkinter.Entry(pframe,</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;">+ pframe.pNaiveEntry = tkinter.Entry(pframe,</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> textvariable=self.pNaive,</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> width=8)</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;">- pframe.pBonfEntry = Tkinter.Entry(pframe,</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;">+ pframe.pBonfEntry = tkinter.Entry(pframe,</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"> textvariable=self.pBonf,</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> width=8)</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pframe.pBHEntry = Tkinter.Entry(pframe,</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pframe.pBHEntry = tkinter.Entry(pframe,</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> textvariable=self.pBH,</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> width=8)</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pframe.pPWEntry = Tkinter.Entry(pframe,</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pframe.pPWEntry = tkinter.Entry(pframe,</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> textvariable=self.pPW,</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> width=8)</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;">- pframe.pEPWEntry = Tkinter.Entry(pframe,</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;">+ pframe.pEPWEntry = tkinter.Entry(pframe,</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> textvariable=self.pEPW,</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> width=8)</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pframe.pPermEntry = Tkinter.Entry(pframe,</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pframe.pPermEntry = tkinter.Entry(pframe,</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> textvariable=self.pPerm,</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> width=8)</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> </span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="p">@@ -524,9 +524,9 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> """</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> Placeholder button. Planned short information about the method</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> """</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- topwin = Tkinter.Toplevel(self)</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ topwin = tkinter.Toplevel(self)</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> button = \</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Button(topwin,</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Button(topwin,</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> text=str("https://github.com/AdmiralenOla/Scoary"))</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> button.pack()</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> </span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="p">@@ -535,7 +535,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> Browse button for gene presence absence field</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> """</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> myfile = \</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tkFileDialog.askopenfilename(</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.filedialog.askopenfilename(</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> filetypes=[('comma-separated values', '.csv'),</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> ('all files','.*')])</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> self.GPAentryVariable.set(myfile)</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="p">@@ -545,7 +545,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> Browse button for traits field</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> """</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"> myfile = \</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tkFileDialog.askopenfilename(</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.filedialog.askopenfilename(</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> filetypes=[('comma-separated values', '.csv'),</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> ('all files','.*')])</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> self.TraitsentryVariable.set(myfile)</span>
</pre>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="p">@@ -555,7 +555,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"> Browse button for tree field</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> """</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> myfile = \</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tkFileDialog.askopenfilename(</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.filedialog.askopenfilename(</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> filetypes=[('newick tree files', '.nwk'),</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> ('all files','.*')])</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> self.TreeentryVariable.set(myfile)</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="p">@@ -565,7 +565,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"> Browse button for isolate restriction field</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> """</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> myfile = \</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tkFileDialog.askopenfilename(</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.filedialog.askopenfilename(</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> filetypes=[('comma-separated values','.csv'),</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> ('all files','.*')])</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> self.RestrictVariable.set(myfile) </span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="p">@@ -574,7 +574,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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594
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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"> Browse button for choosing output dir</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="gd" style="color: #000; background-color: #fdd;">- mydir = tkFileDialog.askdirectory(mustexist=True)</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mydir = tkinter.filedialog.askdirectory(mustexist=True)</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> self.Outputdir.set(mydir)</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> </span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"> def HelpButton(self):</span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="p">@@ -790,7 +790,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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<td class="diff-line-num new new_line" data-linenumber="603" 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">
603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"> if str(SE) == "0":</span>
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<td class="diff-line-num new new_line" data-linenumber="604" 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">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> print("Analysis complete!")</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"> else:</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Fatal error: %s" % str(SE))</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Fatal error: %s" % str(SE)))</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> </span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> # Listen to stdout and update statusbar</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="611" 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">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="p">@@ -800,7 +800,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="613" 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">
613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"> Initialize logo</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> """</span>
</pre>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- photo=Tkinter.PhotoImage(data=self.Photobase64())</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ photo=tkinter.PhotoImage(data=self.Photobase64())</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> self.logocanvas.img = photo</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"> self.logocanvas.create_image(0,0,anchor='nw',image=photo)</span>
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<td class="diff-line-num new new_line" data-linenumber="619" 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">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> </span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="p">@@ -946,7 +946,7 @@</span> class ScoaryGUI(Tkinter.Tk):</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> """</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"> return photo</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> </span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class StdoutToLabel(Tkinter.Label):</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class StdoutToLabel(tkinter.Label):</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> """</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"> The special widget that listens to sys.stdout and updates its</span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"> label accordingly. This widget also owns the progressbar it is</span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="p">@@ -956,7 +956,7 @@</span> class StdoutToLabel(Tkinter.Label):</span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"> def __init__(self, widget, progressbar=None, width='default'):</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Tkinter.Label.__init__(self)</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tkinter.Label.__init__(self)</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> self.defstdout = sys.stdout</span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> self.widget = widget</span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> self.progressbar = progressbar</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scoary/classes.py</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scoary/classes.py</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</span> class Matrix:</span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> self.undef = sys.maxsize</span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> self.dim = int(dim)</span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"> self.data = []</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(self.dim):</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(self.dim):</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> self.data.append(self.dim * [elm])</span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> def __getitem__(self, i):</span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="p">@@ -87,8 +87,8 @@</span> class Matrix:</span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> def __str__(self):</span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> s = ""</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(self.dim):</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(self.dim):</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(self.dim):</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(self.dim):</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"> s += str(self.data[i][j]) + " "</span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> s += "\n"</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> return s.strip("\n")</span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"><span class="p">@@ -106,7 +106,7 @@</span> class QuadTree:</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"> self.dim = dim</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"> n = self.dim + self.dim % 2</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"> if names is None:</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- names = [str(x) for x in xrange(dim)]</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ names = [str(x) for x in range(dim)]</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"> self.names = names</span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"> self.level = []</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"> while n > 1:</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"><span class="p">@@ -129,7 +129,7 @@</span> class QuadTree:</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> if len(curr_row) % 2 == 1:</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> curr_row.append(self.undef)</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"> next_row = []</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(len(curr_row)):</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(len(curr_row)):</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> l[i][j] = curr_row[j]</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> if j % 2 == 1:</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> next_row.append(self.quad_min(i, j, l))</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="p">@@ -145,7 +145,7 @@</span> class QuadTree:</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> if len(curr_col) % 2 == 1:</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> curr_col.append(self.undef)</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> next_col = []</span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(len(curr_col)):</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(curr_col)):</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> l[i][j] = curr_col[i]</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> if i % 2 == 1:</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> next_col.append(self.quad_min(i, j, l))</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="p">@@ -588,8 +588,8 @@</span> class Tip:</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> self.maxvalues[condition] = 0</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> else:</span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> self.maxvalues[condition] = -1</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.max_propairs = {k: v for (k, v) in self.maxvalues.items()}</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.max_antipairs = {k: v for (k, v) in self.maxvalues.items()}</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.max_propairs = {k: v for (k, v) in list(self.maxvalues.items())}</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.max_antipairs = {k: v for (k, v) in list(self.maxvalues.items())}</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"> </span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"> if __name__ == '__main__':</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> pass</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scoary/methods.py</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scoary/methods.py</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"> </span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> # Script for associating Roary output with phenotypic trait (+/-)</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="p">@@ -380,7 +380,7 @@</span> def Csv_to_dic_Roary(genefile, delimiter</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> </span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"> # Move forwards from startcol to find correct startcol</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> if strains[0] in Roarycols and roaryfile:</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for c in xrange(len(strains)):</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for c in range(len(strains)):</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"> if strains[c] not in Roarycols:</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"> correctstartcol = startcol + c</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"> break</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="p">@@ -397,7 +397,7 @@</span> def Csv_to_dic_Roary(genefile, delimiter</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> Firstcols = header[:startcol][::-1]</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> minus = 0</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> Censored_isolates = []</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for c in xrange(len(Firstcols)):</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for c in range(len(Firstcols)):</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"> if Firstcols[c] not in Roarycols:</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> minus += 1</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> Censored_isolates.append(Firstcols[c])</span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="p">@@ -415,7 +415,7 @@</span> def Csv_to_dic_Roary(genefile, delimiter</span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"> </span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> if allowed_isolates is not None:</span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> strain_names_allowed = [val for val in strains</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if val in allowed_isolates.keys()]</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if val in list(allowed_isolates.keys())]</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"> else:</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> strain_names_allowed = strains</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"> </span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="p">@@ -469,9 +469,9 @@</span> def Csv_to_dic_Roary(genefile, delimiter</span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> # between strains.</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"> zero_ones_line = []</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"> </span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for strain in xrange(len(strains)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="738" 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">
738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for strain in range(len(strains)):</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"> if (allowed_isolates is not None):</span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if strains[strain] not in allowed_isolates.keys():</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if strains[strain] not in list(allowed_isolates.keys()):</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"> continue</span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"> if q[startcol + strain] in ["", "0", "-"]:</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"> # If the gene is not present, AND The isolate is allowed</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="p">@@ -499,7 +499,7 @@</span> def Csv_to_dic_Roary(genefile, delimiter</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"> # Transpose list for distance calculation purposes</span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> if writereducedset:</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"> file.close()</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- zero_ones_matrix = list(map(list, zip(*zero_ones_matrix)))</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ zero_ones_matrix = list(map(list, list(zip(*zero_ones_matrix))))</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"> </span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"> return {"Roarydic": r,</span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"> "Zero_ones_matrix": zero_ones_matrix,</span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"><span class="p">@@ -520,8 +520,8 @@</span> def ReduceSet(genefile, delimiter, grabc</span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"> delimiter=delimiter)</span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> header = next(csvfile)</span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"> allowed_indexes = list(range(startcol))</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for c in xrange(len(header)):</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if header[c] in allowed_isolates.keys():</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for c in range(len(header)):</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if header[c] in list(allowed_isolates.keys()):</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> allowed_indexes.append(c)</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"> </span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"> log.info("Writing gene presence absence file for the reduced set of "</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="p">@@ -556,8 +556,8 @@</span> def Csv_to_dic(csvfile, delimiter, allow</span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"> if len(tab) < 2:</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> sys.exit("Please check that your traits file is formatted "</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"> "properly and contains at least one trait")</span>
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<td class="diff-line-num new new_line" data-linenumber="769" 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">
769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for num_trait in xrange(1, len(tab)):</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p = dict(zip(tab[0], tab[num_trait]))</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for num_trait in range(1, len(tab)):</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p = dict(list(zip(tab[0], tab[num_trait])))</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"> if "" in p:</span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"> name_trait = p[""]</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> del p[""]</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"><span class="p">@@ -571,26 +571,26 @@</span> def Csv_to_dic(csvfile, delimiter, allow</span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"> # Filter so that only allowed isolates are included</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> if allowed_isolates is not None:</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"> p = {strain: indicator for (strain, indicator) in </span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- list(p.items()) if strain in allowed_isolates.keys()}</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ list(p.items()) if strain in list(allowed_isolates.keys())}</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"> # Stop if unknown character found in traits file</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"> allowed_values = ["0","1","NA",".","-"," ",""]</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not all([x in allowed_values for x in p.values()]):</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not all([x in allowed_values for x in list(p.values())]):</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"> sys.exit("Unrecognized character found in trait file. Allowed "</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"> "values (no commas): %s" % str(",".join(allowed_values)))</span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"> # Remove isolates with missing values, but only for the </span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"> # trait for which they are missing</span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ("NA" in p.values() </span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- or "-" in p.values() </span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- or "." in p.values()</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- or " " in p.values()</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- or "" in p.values()):</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ("NA" in list(p.values()) </span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ or "-" in list(p.values()) </span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ or "." in list(p.values())</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ or " " in list(p.values())</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ or "" in list(p.values())):</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"> log.warning("WARNING: Some isolates have missing values for "</span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"> "trait %s. Missing-value isolates will not be counted in "</span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"> "association analysis towards this trait." </span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"> % str(name_trait))</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"> p_filt = {strain: indicator for (strain, indicator) in </span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p.items() if indicator not in ["NA","-","."," ",""]}</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Prunedic[name_trait] = [k for (k,v) in p.items() if</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ list(p.items()) if indicator not in ["NA","-","."," ",""]}</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Prunedic[name_trait] = [k for (k,v) in list(p.items()) if</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"> v in ["NA","-","."," ",""]]</span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"> #p = p_filt</span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"> else:</span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"><span class="p">@@ -599,14 +599,14 @@</span> def Csv_to_dic(csvfile, delimiter, allow</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"> # Remove isolates that did not have rows in the trait file but</span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"> # that were allowed by the GPA file/restrict_to</span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"> #if not all(s in p.keys() for s in strains):</span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not all(s in p.keys() for s in strains):</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not all(s in list(p.keys()) for s in strains):</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"> log.error("ERROR: Some isolates in your gene presence "</span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"> "absence file were not represented in your traits file. "</span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"> "These will count as MISSING data and will not be included."</span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"> )</span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"> Prunedic[name_trait] += [s for s in strains if</span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s not in p.keys() and</span></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s not in list(p.keys()) and</span></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"> s not in Prunedic[name_trait]]</span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"> r[name_trait] = p_filt</span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"> Prunedic[name_trait] += [None]</span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"><span class="p">@@ -632,7 +632,7 @@</span> def CreateTriangularDistanceMatrix(zeroo</span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> nstrains = int((1 + (1 + 8*len(hamming_distances))**0.5)/2)</span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"> TriangularDistanceMatrix = []</span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"> Strain_names = []</span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(nstrains):</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(nstrains):</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"> # Adding the maximum relative hamming distance to prevent </span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"> # Quadtree algorithm to pick a pair where i = j</span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"> add = [1] </span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"><span class="p">@@ -650,8 +650,8 @@</span> def PopulateQuadTreeWithDistances(TDM):</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"> First creates a Quadmatrix, so not really optimized.</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"> """</span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"> Quadmatrix = Matrix(dim=len(TDM["matrix"]))</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(Quadmatrix.dim):</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(i, Quadmatrix.dim):</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(Quadmatrix.dim):</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(i, Quadmatrix.dim):</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"> try:</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"> Quadmatrix[i][j] = \</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> Quadmatrix[j][i] = TDM["matrix"][i][(j-i)]</span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"><span class="p">@@ -660,7 +660,7 @@</span> def PopulateQuadTreeWithDistances(TDM):</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"> "Quadtree with pairwise distances. Please "</span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"> "report this bug to olbb@fhi.no")</span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"> PopulatedQuadtree = QuadTree(Quadmatrix.dim, names=TDM["names"])</span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(Quadmatrix.dim):</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(Quadmatrix.dim):</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"> PopulatedQuadtree.insert_row(i, Quadmatrix[i])</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"> return PopulatedQuadtree</span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"> </span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"><span class="p">@@ -683,7 +683,7 @@</span> def upgma(d):</span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"> new_cluster = [cluster[i], cluster[j]]</span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"> new_size = size[i] + size[j]</span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"> new_dist = []</span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k in xrange(d.dim):</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k in range(d.dim):</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"> if cluster[k] is None:</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"> new_dist.append(1)</span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"> else:</span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"><span class="p">@@ -906,7 +906,7 @@</span> def Setup_results(genedic, traitsdic, co</span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"> # Note: Changed from step-down to step-up</span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"> # (from least significant to most significant)</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"> tie = [s_p_v[i-1][1] == s_p_v[i][1] for i in</span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- xrange(1, len(s_p_v))]</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ range(1, len(s_p_v))]</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"> # Initialize dics of corrected p values</span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"> # bh_c_p_v = abbreviation for bh_corrected_p_values</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"> bh_c_p_v = {}</span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"><span class="p">@@ -1074,8 +1074,8 @@</span> def StoreTraitResult(Trait, Traitname, m</span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"> # results list</span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"> </span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"> if multithreaded:</span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- domains = [list(xrange(tnum, num_results, num_threads)) </span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for tnum in xrange(num_threads)]</span></span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ domains = [list(range(tnum, num_results, num_threads)) </span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for tnum in range(num_threads)]</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"> # The Progress variable holds the total progress status of </span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"> # the subprocesses. It is locked, but can be written to by </span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"> # all subprocs</span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"><span class="p">@@ -1089,14 +1089,14 @@</span> def StoreTraitResult(Trait, Traitname, m</span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"> # Need to make a copy of dict to prevent then from pointing </span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"> # to the same object</span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="diff"> all_args = [ (domains[x], dict(argumentlist)) </span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for x in xrange(len(domains)) ] </span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for x in range(len(domains)) ] </span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="diff"> </span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="diff"> Threadresults = pool.imap(PairWiseComparisons,all_args)</span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="diff"> </span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="diff"> pool.close()</span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="diff"> pool.join()</span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"> else:</span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- domains = list(xrange(num_results))</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ domains = list(range(num_results))</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="diff"> argumentlist = {"si":sort_instructions,"tree":upgmatree,</span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="diff"> "GTC": GTC[Traitname],"cutoffs": cutoffs,</span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"> "cp": cut_possibilities,"perm":permutations,</span>
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<td class="diff-line-num new new_line" data-linenumber="904" 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">
904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"><span class="p">@@ -1115,7 +1115,7 @@</span> def StoreTraitResult(Trait, Traitname, m</span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"> Filteredresults = {}</span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"> Threadresults = list(Threadresults)</span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="diff"> </span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for thread in xrange(num_threads):</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for thread in range(num_threads):</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"> for currentgene in Threadresults[thread]:</span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="diff"> Filteredresults[currentgene] = \</span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="diff"> Threadresults[thread][currentgene]</span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="diff"><span class="p">@@ -1141,7 +1141,7 @@</span> def StoreTraitResult(Trait, Traitname, m</span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="diff"> </span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="diff"> log.info("Storing results to file") </span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="diff"> num_filteredresults = min(num_results, len(Filteredresults))</span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for x in xrange(num_filteredresults):</span></span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for x in range(num_filteredresults):</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="diff"> currentgene = sort_instructions[x]</span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="diff"> </span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="diff"> # Final check that the currentgene passes all filters</span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="diff"><span class="p">@@ -1345,7 +1345,7 @@</span> def Permute(tree, GTC, permutations, cut</span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="diff"> proceed = False</span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="diff"> </span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="diff"> if proceed:</span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(permutations):</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(permutations):</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="diff"> # Make a permutation using random.shuffle</span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="diff"> PermutedGTC = PermuteGTC(GTCcopy)</span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="diff"> # Send new set to phylotree</span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="diff"><span class="p">@@ -1374,7 +1374,7 @@</span> def PermuteGTC(GTC):</span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="diff"> labels have been swapped</span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="diff"> """</span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="diff"> # Set of trait labels to distribute</span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- trait_labels = [s[-1] for s in GTC.values()]</span></span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ trait_labels = [s[-1] for s in list(GTC.values())]</span></span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="diff"> # Shuffle list of labels</span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="diff"> random.shuffle(trait_labels)</span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="diff"> for isolate in GTC:</span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="diff"><span class="p">@@ -1480,7 +1480,7 @@</span> def filtrationoptions(cutoffs, collapse)</span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="diff"> "EPW": "Pairwise comparison (Entire range)",</span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="diff"> "P": "Empirical p-value (permutation-based)"}</span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="diff"> filters = [str(translation[k]) + ": " + str(v)</span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k,v in cutoffs.items()] </span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k,v in list(cutoffs.items())] </span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="diff"> filters.append("Collapse genes: " + str(collapse) + "\n\n")</span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="diff"> filters = ["-- Filtration options --"] + filters</span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="diff"> </span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="diff"><span class="p">@@ -1528,7 +1528,7 @@</span> def grabcoltype(string):</span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="diff"> bydash = s.split("-")</span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="diff"> if not (int(bydash[1]) > int(bydash[0])):</span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="diff"> raise</span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- add = range(int(bydash[0]), int(bydash[1]))</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ add = list(range(int(bydash[0]), int(bydash[1])))</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="diff"> returnlist += list(add)</span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="diff"> except:</span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="diff"> sys.exit("Could not understand --include_input_columns "</span>
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<td class="diff-line-num new new_line" data-linenumber="958" 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">
958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scoary/vcf2scoary.py</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scoary/vcf2scoary.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="960" 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">
960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="961" 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">
961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="962" 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">
962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="diff"> </span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="diff"> # Script to search vcf files for mutations within specific coordinates</span>
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<td class="diff-line-num new new_line" data-linenumber="966" 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">
966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="diff"><span class="p">@@ -116,7 +116,7 @@</span> def main():</span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="968" 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">
968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="diff"> line = next(lines)</span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="diff"> except StopIteration:</span>
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<td class="diff-line-num new new_line" data-linenumber="970" 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">
970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(traceback.print_exc())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="971" 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">
971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((traceback.print_exc()))</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="diff"> sys.exit("ERROR: There appears to be only metainformation "</span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="diff"> "(lines starting with ##) in your VCF file.")</span>
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<td class="diff-line-num new new_line" data-linenumber="974" 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">
974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="diff"> # Get metainfo from file</span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="diff"><span class="p">@@ -145,11 +145,11 @@</span> def main():</span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="diff"> print("WARNING: A VCF format other than 4.x detected."</span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="diff"> " File parsing may proceed with errors.")</span>
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<td class="diff-line-num new new_line" data-linenumber="978" 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">
978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="979" 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">
979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("VCF version %s detected" % vcfversion)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="980" 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">
980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("VCF version %s detected" % vcfversion))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="981" 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">
981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="diff"> except:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="982" 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">
982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="diff"> print("WARNING: Could not detect VCF format. Expected "</span>
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<td class="diff-line-num new new_line" data-linenumber="983" 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">
983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="diff"> "v4.x. File parsing may proceed with errors.")</span>
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<td class="diff-line-num new new_line" data-linenumber="984" 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">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(traceback.print_exc())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="985" 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">
985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((traceback.print_exc()))</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="diff"> </span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="diff"> # Check that genotype fields have a single allele</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="988" 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">
988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="diff"> if metainfo["##FORMAT"]["GT"]["Number"] != "1":</span>
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<td class="diff-line-num new new_line" data-linenumber="989" 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">
989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="diff"><span class="p">@@ -213,7 +213,7 @@</span> def fixdummy(line,c):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="990" 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">
990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="991" 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">
991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="diff"> newline[x] = "0"</span>
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<td class="diff-line-num new new_line" data-linenumber="992" 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">
992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="diff"> except ValueError:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="993" 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">
993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(newline, c)</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((newline, c))</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="diff"> sys.exit(-1)</span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="diff"> return newline</span>
</pre>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="diff"> </span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_scoary_output.py</span></span>
</pre>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_scoary_output.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1000" 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">
1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="diff"><span class="p">@@ -30,94 +30,94 @@</span> for Test in ["1","2","4"]:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1001" 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">
1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1002" 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">
1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="diff"> assert data[0] == reference[0]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1003" 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">
1003
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1003" class="line" lang="diff"> except AssertionError:</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1004" 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">
1004
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1004" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 0: %s %s" % (Test, data[0], reference[0]))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1005" 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">
1005
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1005" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 0: %s %s" % (Test, data[0], reference[0])))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1006" 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">
1006
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1006" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1007" 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">
1007
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1007" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1008" 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">
1008
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1008" class="line" lang="diff"> assert data[1] == reference[1]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1009" 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">
1009
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1009" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1010" 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">
1010
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1010" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 1: %s %s" % (Test, data[1], reference[1]))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1011" 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">
1011
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1011" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 1: %s %s" % (Test, data[1], reference[1])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1012" 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">
1012
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1012" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1013" 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">
1013
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1013" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1014" 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">
1014
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1014" class="line" lang="diff"> assert data[2] == reference[2]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1015" 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">
1015
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1015" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1016" 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">
1016
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1016" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 2: %s %s" % (Test, data[2], reference[2]))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1017" 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">
1017
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1017" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 2: %s %s" % (Test, data[2], reference[2])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1018" 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">
1018
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1018" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1019" 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">
1019
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1019" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1020" 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">
1020
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1020" class="line" lang="diff"> assert int(data[3]) == reference[3]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1021" 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">
1021
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1021" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1022" 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">
1022
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1022" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 3: %s %s" % (Test, data[3], str(reference[3])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1023" 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">
1023
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1023" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 3: %s %s" % (Test, data[3], str(reference[3]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1024" 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">
1024
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1024" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1025" 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">
1025
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1025" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1026" 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">
1026
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1026" class="line" lang="diff"> assert int(data[4]) == reference[4]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1027" 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">
1027
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1027" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1028" 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">
1028
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1028" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 4: %s %s" % (Test, data[4], str(reference[4])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1029" 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">
1029
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1029" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 4: %s %s" % (Test, data[4], str(reference[4]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1030" 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">
1030
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1030" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1031" 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">
1031
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1031" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1032" 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">
1032
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1032" class="line" lang="diff"> assert int(data[5]) == reference[5]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1033" 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">
1033
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1033" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1034" 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">
1034
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1034" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 5: %s %s" % (Test, data[5], str(reference[5])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1035" 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">
1035
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1035" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 5: %s %s" % (Test, data[5], str(reference[5]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1036" 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">
1036
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1036" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1037" 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">
1037
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1037" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1038" 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">
1038
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1038" class="line" lang="diff"> assert int(data[6]) == reference[6]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1039" 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">
1039
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1039" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1040" 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">
1040
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1040" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 6: %s %s" % (Test, data[6], str(reference[6])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1041" 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">
1041
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1041" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 6: %s %s" % (Test, data[6], str(reference[6]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1042" 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">
1042
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1042" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1043" 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">
1043
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1043" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1044" 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">
1044
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1044" class="line" lang="diff"> assert abs(float(data[7]) - reference[7]) <= 0.01</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1045" 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">
1045
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1045" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1046" 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">
1046
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1046" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 7: %s %s" % (Test, data[7], str(reference[7])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1047" 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">
1047
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1047" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 7: %s %s" % (Test, data[7], str(reference[7]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1048" 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">
1048
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1048" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1049" 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">
1049
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1049" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1050" 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">
1050
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1050" class="line" lang="diff"> assert abs(float(data[8]) - reference[8]) <= 0.01</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1051" 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">
1051
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1051" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1052" 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">
1052
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1052" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 8: %s %s" % (Test, data[8], str(reference[8])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1053" 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">
1053
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1053" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 8: %s %s" % (Test, data[8], str(reference[8]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1054" 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">
1054
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1054" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1055" 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">
1055
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1055" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1056" 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">
1056
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1056" class="line" lang="diff"> assert abs(float(data[9]) - reference[9]) <= 0.1</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1057" 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">
1057
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1057" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1058" 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">
1058
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1058" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 9: %s %s" % (Test, data[9], str(reference[9])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1059" 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">
1059
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1059" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 9: %s %s" % (Test, data[9], str(reference[9]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1060" 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">
1060
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1060" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1061" 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">
1061
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1061" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1062" 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">
1062
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1062" class="line" lang="diff"> assert abs(float(data[10]) - reference[10]) <= 1E-15</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1063" 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">
1063
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1063" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1064" 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">
1064
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1064" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 10: %s %s" % (Test, data[10], str(reference[10])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1065" 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">
1065
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1065" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 10: %s %s" % (Test, data[10], str(reference[10]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1066" 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">
1066
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1066" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1067" 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">
1067
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1067" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1068" 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">
1068
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1068" class="line" lang="diff"> assert abs(float(data[11]) - reference[11]) <= 1E-12</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1069" 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">
1069
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1069" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1070" 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">
1070
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1070" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 11: %s %s" % (Test, data[11], str(reference[11])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1071" 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">
1071
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1071" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 11: %s %s" % (Test, data[11], str(reference[11]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1072" 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">
1072
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1072" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1073" 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">
1073
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1073" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1074" 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">
1074
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1074" class="line" lang="diff"> assert abs(float(data[12]) - reference[12]) <= 1E-12</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1075" 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">
1075
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1075" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1076" 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">
1076
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1076" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 12: %s %s" % (Test, data[12], str(reference[12])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1077" 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">
1077
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1077" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 12: %s %s" % (Test, data[12], str(reference[12]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1078" 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">
1078
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1078" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1079" 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">
1079
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1079" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1080" 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">
1080
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1080" class="line" lang="diff"> if not Test == "2":</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1081" 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">
1081
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1081" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1082" 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">
1082
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1082" class="line" lang="diff"> assert int(data[13]) == reference[13]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1083" 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">
1083
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1083" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1084" 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">
1084
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1084" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 13: %s %s" % (Test, data[13], str(reference[13])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1085" 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">
1085
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1085" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 13: %s %s" % (Test, data[13], str(reference[13]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1086" 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">
1086
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1086" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1087" 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">
1087
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1087" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1088" 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">
1088
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1088" class="line" lang="diff"> assert int(data[14]) == reference[14]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1089" 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">
1089
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1089" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1090" 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">
1090
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1090" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 14: %s %s" % (Test, data[14], str(reference[14])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1091" 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">
1091
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1091" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 14: %s %s" % (Test, data[14], str(reference[14]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1092" 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">
1092
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1092" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1093" 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">
1093
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1093" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1094" 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">
1094
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1094" class="line" lang="diff"> assert int(data[15]) == reference[15]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1095" 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">
1095
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1095" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1096" 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">
1096
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1096" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 15: %s %s" % (Test, data[15], str(reference[15])))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1097" 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">
1097
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1097" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 15: %s %s" % (Test, data[15], str(reference[15]))))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1098" 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">
1098
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1098" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1099" 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">
1099
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1099" class="line" lang="diff"> try:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1100" 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">
1100
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1100" class="line" lang="diff"> assert abs(float(data[16]) - reference[16]) <= 1E-9</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="1101" 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">
1101
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1101" class="line" lang="diff"> except AssertionError:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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<td class="diff-line-num new new_line" data-linenumber="1102" 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">
1102
</td>
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 16: %s %s" % (Test, data[16], str(reference[16])))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1103" 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">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 16: %s %s" % (Test, data[16], str(reference[16]))))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1104" 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">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="1105" 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">
1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="1106" 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">
1106
</td>
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="diff"> assert abs(float(data[17]) - reference[17]) <= 1E-7</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="1107" 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">
1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="diff"> except AssertionError:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="1108" 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">
1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Not equal at Test %s col 17: %s %s" % (Test, data[17], str(reference[17])))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1109" 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">
1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Not equal at Test %s col 17: %s %s" % (Test, data[17], str(reference[17]))))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1110" 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">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1111" 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">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1112" 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">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="diff"> with open(os.getcwd() + "/mutations_presence_absence.csv" ,"rU") as vcfresfile:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1113" 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">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="diff"><span class="p">@@ -130,8 +130,8 @@</span> with open(os.getcwd() + "/mutations_pres</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1114" 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">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="1115" 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">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="diff"> assert data == referencevcf</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1116" 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">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="diff"> except AssertionError:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="1117" 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">
1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Got: %s" % ",".join(data))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1118" 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">
1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Expected: %s" % ",".join(referencevcf))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1119" 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">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Got: %s" % ",".join(data)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1120" 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">
1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Expected: %s" % ",".join(referencevcf)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1121" 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">
1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="diff"> print("VCF conversion did not produce the expected output")</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1122" 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">
1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="diff"> sys.exit(-1)</span>
</pre>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/scoary/compare/902691ea72f00079155953988bae8a0b3103aa0f...f635c072de0321d257461571177818af056c4822#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/scoary/compare/902691ea72f00079155953988bae8a0b3103aa0f...f635c072de0321d257461571177818af056c4822#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL = C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="6" 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span> --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span> --buildsystem=pybuild</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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