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GitLab

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<h3>

Nilesh Patra pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/tnseq-transit">Debian Med / tnseq-transit</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4">ad0cdd39</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-12-24T23:40:37+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.1</pre>

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<h4>11 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

CHANGELOG.md

</a>

</li>

<li class="file-stats">

<a href="#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">

src/pytransit/__init__.py

</a>

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<li class="file-stats">

<a href="#8f7b871a787b5d5c5b3a11bed95337c59a510906">

src/pytransit/analysis/gi.py

</a>

</li>

<li class="file-stats">

<a href="#a522d0d990a6ccfbb24eba81a727b32c79e5f81a">

src/pytransit/analysis/gumbel.py

</a>

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<li class="file-stats">

<a href="#00356195138da970d79b40310349b42befe9abe3">

src/pytransit/analysis/hmm.py

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<li class="file-stats">

<a href="#c8957f2356d9e8d37d053848a519d268c0da4500">

src/pytransit/analysis/rankproduct.py

</a>

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<li class="file-stats">

<a href="#46073ef784cdc338b0714d64bb6fd29c8fbdaf90">

src/pytransit/analysis/resampling.py

</a>

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<li class="file-stats">

<a href="#bc8898d1d2d3504ac8c72cd9edc38508899cca04">

src/pytransit/analysis/tn5gaps.py

</a>

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<li class="file-stats">

<a href="#7296872bff29c67bcf0f86ab4bc0ce8bb7e016be">

src/pytransit/analysis/utest.py

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<a href="#de3c043793d996a85ac3d6982bac37682e8c47bc">

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+

src/pytransit/data/README.md

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<a href="#9386e7617c74b0243bc02213115ce1779653c401">

<span class="new-file">

+

src/pytransit/data/smeg_GO_terms.txt

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</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Change log</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">All notable changes to this project will be documented in this file.</span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_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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<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="markdown"></span>

</pre>

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<td class="diff-line-num new old_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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<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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.1 2020-12-22</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(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="LC7" class="line" lang="markdown"><span class="p"> -</span> maintenance release</span>

</pre>

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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="markdown"><span class="p">  -</span> fixed a bug in the GUI caused by changes in wxPython 4.1.0</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">  -</span> added GO terms for M. smegmatis in the data directory for doing pathway analysis</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.0 2020-10-26</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>

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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="markdown"><span class="p"> -</span> improvements to pathway_enrichment analysis</span>

</pre>

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<br>

</li>

<li id="176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4"><strong>src/pytransit/__init__.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,6 @@</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"transit_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tnseq_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"norm_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stat_tools"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.2.<span class="idiff left right">0</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.2.<span class="idiff left right">1</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[TRANSIT]"</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span></pre>

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<br>

</li>

<li id="8f7b871a787b5d5c5b3a11bed95337c59a510906">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#8f7b871a787b5d5c5b3a11bed95337c59a510906"><strong>src/pytransit/analysis/gi.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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="115" 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">@@ -115,19 +115,19 @@ class GIGUI(base.AnalysisGUI):</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Samples</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">giSampleLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">giSampleText</span><span class="p">,</span> <span class="n" style="color: #333;">sampleSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">giPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Samples:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"10000"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of samples to take when estimating the distributions of means. More samples give more accurate estimates at the cost of computation time."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># ROPE</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="122" 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="LC122" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">giROPELabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">giROPEText</span><span class="p">,</span> <span class="n" style="color: #333;">ROPESizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">giPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"ROPE:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"0.5"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Region of Practical Equivalence. Area around 0 (i.e. 0.0 +/- ROPE) that defines changes in enrichment (delta-log2FC) that are NOT of interest. Can be thought of as the area representing a null-hypothesis."</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">ROPESizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">ROPESizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Norm</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">        <span class="n" style="color: #333;">giNormChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"TTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nzmean"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"totreads"</span><span class="p">,</span> <span class="s" style="color: #d14;">u'zinfnb'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'quantile'</span><span class="p">,</span> <span class="s" style="color: #d14;">u"betageom"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nonorm"</span> <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">giNormLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">giNormChoice</span><span class="p">,</span> <span class="n" style="color: #333;">normSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">giPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Normalization:"</span><span class="p">,</span> <span class="n" style="color: #333;">giNormChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Choice of normalization method. The default choice, 'TTR', normalizes datasets to have the same expected count (while not being sensative to outliers). Read documentation for a description other methods. "</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">        <span class="n" style="color: #333;">giSizer</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">mainSizer1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<br>

</li>

<li id="a522d0d990a6ccfbb24eba81a727b32c79e5f81a">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#a522d0d990a6ccfbb24eba81a727b32c79e5f81a"><strong>src/pytransit/analysis/gumbel.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" 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="99" 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">@@ -99,25 +99,25 @@ class GumbelGUI(base.AnalysisGUI):</td>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Samples</span></span>

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<td class="diff-line-num old_line" data-linenumber="101" 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="LC101" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">gumbelSampleLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">gumbelSampleText</span><span class="p">,</span> <span class="n" style="color: #333;">sampleSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">gumbelPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Samples:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"10000"</span><span class="p">,</span> <span class="s" style="color: #d14;">"These are the number of samples to take when estimating the parameters. More samples give more accurate estimates of the parameters at the cost of computation time."</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(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="102" style="width: 35px; color: rgba(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="LC102" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" 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">

103

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<td class="diff-line-num new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" 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">

104

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<td class="diff-line-num new_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Burn-In </span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" 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">

105

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<td class="diff-line-num new_line" data-linenumber="105" 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="LC105" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">gumbelBurninLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">gumbelBurninText</span><span class="p">,</span> <span class="n" style="color: #333;">burninSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">gumbelPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Burn-In:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"500"</span><span class="p">,</span> <span class="s" style="color: #d14;">"These are the number of samples to take before  beginning to estimate the parameters. Allows the MCMC sampler to 'converge' to the true parameter space. More samples give more accurate estimates of the parameters at the cost of computation time."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">burninSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(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="106" style="width: 35px; color: rgba(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="LC106" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">burninSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" 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">

107

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<td class="diff-line-num new_line" data-linenumber="107" 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">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" 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="108" 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="LC108" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Trim</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" 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="109" 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="LC109" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">gumbelTrimLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">gumbelTrimText</span><span class="p">,</span> <span class="n" style="color: #333;">trimSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">gumbelPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Trim:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"The MCMC sample will keep every i-th sample. A value of '1' will take all samples. Larger values will reduces autocorrelation at the cost of a substantial cost in computation time."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">trimSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(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="110" style="width: 35px; color: rgba(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="LC110" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">trimSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" 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="111" 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">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="112" 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="112" 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="LC112" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Min Read</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" 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="113" 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="LC113" class="line" lang="python">        <span class="n" style="color: #333;">gumbelReadChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"2"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"3"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"4"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"5"</span> <span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" 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="LC114" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">gumbelReadLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">gumbelReadChoice</span><span class="p">,</span> <span class="n" style="color: #333;">readSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">gumbelPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Minimum Read:"</span><span class="p">,</span> <span class="n" style="color: #333;">gumbelReadChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"This is the minimum number of reads to consider a 'true' insertion. Value of 1 will consider all insertions. Larger values allow the method to ignore spurious insertions which might interrupt a run of non-insertions. Noisy datasets or those with many replicates can beneffit from increasing this."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">readSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">readSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

</pre>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Replicates</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">gumbelRepChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"Sum"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Mean"</span> <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">gumbelRepLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">gumbelRepChoice</span><span class="p">,</span> <span class="n" style="color: #333;">repSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">gumbelPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Replicates:"</span><span class="p">,</span> <span class="n" style="color: #333;">gumbelRepChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Determines how to handle replicates, and their read-counts. When using many replicates, summing read-counts may make spurious counts appear to be significantly large and interrupt a run of non-insertions."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">repSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">repSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span>        </span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python">       </span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">        <span class="n" style="color: #333;">gumbelSection</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">mainSizer1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<br>

</li>

<li id="00356195138da970d79b40310349b42befe9abe3">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#00356195138da970d79b40310349b42befe9abe3"><strong>src/pytransit/analysis/hmm.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" 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="129" 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">@@ -129,18 +129,18 @@ class HMMGUI(base.AnalysisGUI):</td>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">        <span class="n" style="color: #333;">hmmSizer1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">BoxSizer</span><span class="p">(</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">VERTICAL</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#(, , Sizer) = self.defineChoiceBox(hmmPanel, u"", hmmNormChoiceChoices, "")</span></span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#hmmSizer1.Add(Sizer, 1, wx.<span class="idiff left right">ALIGN_CENTER_HORIZONTAL|wx.</span>EXPAND, 5 )</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#hmmSizer1.Add(Sizer, 1, wx.EXPAND, 5 )</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># NORMALIZATION</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python">        <span class="n" style="color: #333;">hmmNormChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"TTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nzmean"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"totreads"</span><span class="p">,</span> <span class="s" style="color: #d14;">u'zinfnb'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'quantile'</span><span class="p">,</span> <span class="s" style="color: #d14;">u"betageom"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nonorm"</span> <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">hmmNormLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">hmmNormChoice</span><span class="p">,</span> <span class="n" style="color: #333;">normSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">hmmPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Normalization:"</span><span class="p">,</span> <span class="n" style="color: #333;">hmmNormChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Choice of normalization method. The default choice, 'TTR', normalizes datasets to have the same expected count (while not being sensative to outliers). Read documentation for a description other methods."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python">        <span class="n" style="color: #333;">hmmSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python">        <span class="n" style="color: #333;">hmmSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># REPLICATE</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">        <span class="n" style="color: #333;">hmmRepChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"Sum"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Mean"</span> <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">hmmRepLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">hmmRepChoice</span><span class="p">,</span> <span class="n" style="color: #333;">repSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">hmmPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Replicates:"</span><span class="p">,</span> <span class="n" style="color: #333;">hmmRepChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Determines how to handle replicates, and their read-counts. When using many replicates, using 'Mean' may be recommended over 'Sum'"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python">        <span class="n" style="color: #333;">hmmSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">repSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python">        <span class="n" style="color: #333;">hmmSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">repSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># LOESS</span></span>

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<br>

</li>

<li id="c8957f2356d9e8d37d053848a519d268c0da4500">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#c8957f2356d9e8d37d053848a519d268c0da4500"><strong>src/pytransit/analysis/rankproduct.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,14 +80,14 @@ class RankProductGUI(base.AnalysisGUI):</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">        </span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># SAMPLES</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">rankproductSampleLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">rankproductSampleText</span><span class="p">,</span> <span class="n" style="color: #333;">sampleSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">rankproductPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Samples:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"10000"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of samples to take when estimating the theoretical rankproduct distribution. Larger samples give more accurate estimates at the cost of computation time."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python">    </span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># NORMALIZATION</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Norm </span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">        <span class="n" style="color: #333;">rankproductNormChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"TTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nzmean"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"totreads"</span><span class="p">,</span> <span class="s" style="color: #d14;">u'zinfnb'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'quantile'</span><span class="p">,</span> <span class="s" style="color: #d14;">u"betageom"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nonorm"</span> <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">rankproductNormLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">rankproductNormChoice</span><span class="p">,</span> <span class="n" style="color: #333;">normSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">rankproductPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Normalization:"</span><span class="p">,</span> <span class="n" style="color: #333;">rankproductNormChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Choice of normalization method. The default choice, 'TTR', normalizes datasets to have the same expected count (while not being sensative to outliers). Read documentation for a description other methods. "</span><span class="p">)</span> </span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python">        <span class="n" style="color: #333;">rankproductSizer</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">mainSizer1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>

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<br>

</li>

<li id="46073ef784cdc338b0714d64bb6fd29c8fbdaf90">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#46073ef784cdc338b0714d64bb6fd29c8fbdaf90"><strong>src/pytransit/analysis/resampling.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,21 +119,21 @@ class ResamplingGUI(base.AnalysisGUI):</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">BoxSizer</span><span class="p">(</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">VERTICAL</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#(, , Sizer) = self.defineChoiceBox(resamplingPanel, u"", u"", "")</span></span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#mainSizer1.Add(Sizer, 1, wx.<span class="idiff left right">ALIGN_CENTER_HORIZONTAL|wx.</span>EXPAND, 5 )</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#mainSizer1.Add(Sizer, 1, wx.EXPAND, 5 )</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Samples</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" 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="LC125" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">resamplingSampleLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">resamplingSampleText</span><span class="p">,</span> <span class="n" style="color: #333;">sampleSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">resamplingPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Samples:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"10000"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of samples to take when estimating the resampling histogram. More samples give more accurate estimates of the p-values at the cost of computation time."</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="127" style="width: 35px; color: rgba(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="LC126" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sampleSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Pseudocount - changing the semantics on 3/5/20</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#(resamplingPseudocountLabel, self.wxobj.resamplingPseudocountText, pseudoSizer) = self.defineTextBox(resamplingPanel, u"Pseudocount:", u"0.0", "Adds pseudo-counts to the each data-point. Useful to dampen the effects of small counts which may lead to deceptively high log-FC.")</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">resamplingPseudocountLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">resamplingPseudocountText</span><span class="p">,</span> <span class="n" style="color: #333;">pseudoSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineTextBox</span><span class="p">(</span><span class="n" style="color: #333;">resamplingPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Pseudocount:"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"0.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Pseudo-counts used in calculating log-fold-chnage. Useful to dampen the effects of small counts which may lead to deceptively high LFC."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">pseudoSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">pseudoSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Norm</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python">        <span class="n" style="color: #333;">resamplingNormChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"TTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nzmean"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"totreads"</span><span class="p">,</span> <span class="s" style="color: #d14;">u'zinfnb'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'quantile'</span><span class="p">,</span> <span class="s" style="color: #d14;">u"betageom"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nonorm"</span> <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">resamplingNormLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">resamplingNormChoice</span><span class="p">,</span> <span class="n" style="color: #333;">normSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">resamplingPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Normalization: "</span><span class="p">,</span> <span class="n" style="color: #333;">resamplingNormChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Choice of normalization method. The default choice, 'TTR', normalizes datasets to have the same expected count (while not being sensative to outliers). Read documentation for a description other methods. "</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>

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<li id="bc8898d1d2d3504ac8c72cd9edc38508899cca04">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#bc8898d1d2d3504ac8c72cd9edc38508899cca04"><strong>src/pytransit/analysis/tn5gaps.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" 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="93" 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">@@ -93,13 +93,13 @@ class Tn5GapsGUI(base.AnalysisGUI):</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Min Read</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python">        <span class="n" style="color: #333;">tn5GapsReadChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"2"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"3"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"4"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"5"</span> <span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" 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="95" 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="LC95" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">tn5GapsReadLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">tn5GapsReadChoice</span><span class="p">,</span> <span class="n" style="color: #333;">readSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">tn5GapsPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Minimum Read:"</span><span class="p">,</span> <span class="n" style="color: #333;">tn5GapsReadChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"This is the minimum number of reads to consider a 'true' insertion. Value of 1 will consider all insertions. Larger values allow the method to ignore spurious insertions which might interrupt a run of non-insertions. Noisy datasets or those with many replicates can beneffit from increasing this."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">readSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(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="LC96" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">readSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">   </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" 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="98" 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="LC98" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" 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="LC99" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Replicates</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" 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="LC100" class="line" lang="python">        <span class="n" style="color: #333;">tn5GapsRepChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"Sum"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Mean"</span> <span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" 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="101" 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="LC101" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">tn5GapsRepLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">tn5GapsRepChoice</span><span class="p">,</span> <span class="n" style="color: #333;">repSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">tn5GapsPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Replicates:"</span><span class="p">,</span> <span class="n" style="color: #333;">tn5GapsRepChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Determines how to handle replicates, and their read-counts. When using many replicates, summing read-counts may make spurious counts appear to be significantly large and interrupt a run of non-insertions."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">repSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(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="102" style="width: 35px; color: rgba(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="LC102" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">repSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="103" 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="LC103" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" 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="104" 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="LC104" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" 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="105" 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="LC105" class="line" lang="python">        <span class="n" style="color: #333;">tn5GapsSection</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">mainSizer1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

</pre>

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</table>

<br>

</li>

<li id="7296872bff29c67bcf0f86ab4bc0ce8bb7e016be">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#7296872bff29c67bcf0f86ab4bc0ce8bb7e016be"><strong>src/pytransit/analysis/utest.py</strong></a>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">BoxSizer</span><span class="p">(</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">VERTICAL</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#(, , Sizer) = self.defineChoiceBox(utestPanel, u"", u"", "")</span></span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#mainSizer1.Add(Sizer, 1, wx.<span class="idiff left right">ALIGN_CENTER_HORIZONTAL|wx.</span>EXPAND, 5 )</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#mainSizer1.Add(Sizer, 1, wx.EXPAND, 5 )</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Norm</span></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python">        <span class="n" style="color: #333;">utestNormChoiceChoices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">u"TTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nzmean"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"totreads"</span><span class="p">,</span> <span class="s" style="color: #d14;">u'zinfnb'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'quantile'</span><span class="p">,</span> <span class="s" style="color: #d14;">u"betageom"</span><span class="p">,</span> <span class="s" style="color: #d14;">u"nonorm"</span> <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">utestNormLabel</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">utestNormChoice</span><span class="p">,</span> <span class="n" style="color: #333;">normSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineChoiceBox</span><span class="p">(</span><span class="n" style="color: #333;">utestPanel</span><span class="p">,</span> <span class="s" style="color: #d14;">u"Normalization:"</span><span class="p">,</span> <span class="n" style="color: #333;">utestNormChoiceChoices</span><span class="p">,</span> <span class="s" style="color: #d14;">"Choice of normalization method. The default choice, 'TTR', normalizes datasets to have the same expected count (while not being sensative to outliers). Read documentation for a description other methods. "</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ALIGN_CENTER_HORIZONTAL</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">wx</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python">        <span class="n" style="color: #333;">mainSizer1</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">normSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">utestSizer</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">mainSizer1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>

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<br>

</li>

<li id="de3c043793d996a85ac3d6982bac37682e8c47bc">

<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/ad0cdd39e7e088baebd489d0a1d59125bde320e4#de3c043793d996a85ac3d6982bac37682e8c47bc"><strong>src/pytransit/data/README.md</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Transit Data directory</span></span>

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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="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">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======================</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="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">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></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="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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;">Files for Pathway Enrichment analysis</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="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">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------------------------</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="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">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">These files can be used for pathway_enrichment analysis.</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="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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">```</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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">+----------+---------+--------------------+--------------------------------------+--------------------------------+</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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">| system   | num cats| applicable methods | associations of genes with roles     | pathway definitions/role names |</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">+==========+=========+====================+======================================+================================+</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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">| COG      | 20      | FET*, GSEA         | H37Rv_COG_roles.dat                  | COG_roles.dat                  |</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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">+----------+---------+--------------------+--------------------------------------+--------------------------------+</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="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">| Sanger   | 153     | FET*, GSEA*        | H37Rv_sanger_roles.dat               | sanger_roles.dat               |</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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">+----------+---------+--------------------+--------------------------------------+--------------------------------+</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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">| GO       | 2545    | FET, GSEA          | H37Rv_GO_terms.txt                   | GO_term_names.dat              |</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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">+----------+---------+--------------------+--------------------------------------+--------------------------------+</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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">|          |         | ONT*               | GO_terms_for_each_Rv.obo-3-11-18.txt | gene_ontology.1_2.3-11-18.obo  |</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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">+----------+---------+--------------------+--------------------------------------+--------------------------------+</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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">```</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">These file are to be used as inputs for the transit pathway_enrichment </span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">command (see the <span class="p">[</span><span class="nv" style="color: #008080;">documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://transit.readthedocs.io/en/latest/transit_methods.html#pathway-enrichment-analysis</span><span class="p">)</span>).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">A file with GO terms for Mycobacterium smegmatis is also included: smeg_GO_terms.txt.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="gh" style="color: #999;">Test files for resampling</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------------</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">These wig files are from the </span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Griffin et al (2011) paper in PLOS Pathogens</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.ncbi.nlm.nih.gov/pubmed/21980284</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">on M. tuberculosis genes required for growth on glycerol.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p"> *</span> glycerol_H37Rv_rep1.wig, glycerol_H37Rv_rep2.wig, glycerol_H37Rv_rep3.wig</span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="p"> *</span> cholesterol_H37Rv_rep1.wig, cholesterol_H37Rv_rep2.wig, cholesterol_H37Rv_rep3.wig</span></pre>

</td>

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</table>

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