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GitLab

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<h3>

Steffen Möller 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/20d19355d501e251533c1e6e708100581caffe85">20d19355</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-01-18T22:46:11+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.2</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

CHANGELOG.md

</a>

</li>

<li class="file-stats">

<a href="#9341fa10457e26d08a7de9ad63515676cf7b621e">

<span class="new-file">

+

src/fitness_defect.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">

src/pytransit/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#8f7b871a787b5d5c5b3a11bed95337c59a510906">

src/pytransit/analysis/gi.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="#07ca99dc668f43ea2451861342e18d287151cf0c">

src/pytransit/analysis/zinb.py

</a>

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<li class="file-stats">

<a href="#e4c47efb9db43431093096e67f5aab587b257ff4">

src/pytransit/doc/source/transit_methods.rst

</a>

</li>

<li class="file-stats">

<a href="#bf71c4ed5781c2e556f922c3622eb4c0faac245f">

src/pytransit/doc/source/transit_overview.rst

</a>

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<li class="file-stats">

<a href="#08b6cc113ef5013285f95a556c9c6c247be98f22">

src/pytransit/export/combined_wig.py

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<li class="file-stats">

<a href="#d0edb611a89a0dab9d0dc046d324f550b89d3d03">

src/pytransit/transit_gui.py

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</ul>

<h4>Changes:</h4>

<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

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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<td class="diff-line-num new_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">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

<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 class="gu" style="color: #800080; font-weight: 600;">## Version 3.0.2 2019-12-21</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="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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<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="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</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">

6

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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="LC6" class="line" lang="markdown"><span class="p"> -</span> Mostly cosmetic fixes</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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<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"><span class="p"> -</span> Updated some command-line and GUI messages</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="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> Updated documentation (especially for GI and resampling)</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="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> Removed "warning: high stderr" from gene status in ZINB</span>

</pre>

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<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">

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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="LC10" class="line" lang="markdown"><span class="p"> -</span> Added LFCs in ZINB output</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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<pre style="margin: 0;">+<span id="LC11" 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">

4

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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;">## Version 3.0.1 2019-08-01</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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" 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 old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="14" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p"> -</span> Add check for python3 (TRANSIT 3+ requires python3.6+)</span>

</pre>

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<br>

</li>

<li id="9341fa10457e26d08a7de9ad63515676cf7b621e">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#9341fa10457e26d08a7de9ad63515676cf7b621e"><strong>src/fitness_defect.py</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(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="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span><span class="p">,</span><span class="n" style="color: #333;">random</span><span class="p">,</span><span class="n" style="color: #333;">numpy</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytransit.tnseq_tools</span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">statsmodels.stats.multitest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fdrcorrection</span></span>

</pre>

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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">

4

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

</pre>

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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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_wig</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python">  <span class="n" style="color: #333;">coords</span><span class="p">,</span><span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"0123456789"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">    <span class="n" style="color: #333;">coord</span><span class="p">,</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">    <span class="n" style="color: #333;">coords</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">coord</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">    <span class="n" style="color: #333;">counts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">cnt</span><span class="p">)</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">coords</span><span class="p">,</span><span class="n" style="color: #333;">counts</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># remove all runs of zeros of length >= W</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_essential_regions</span><span class="p">(</span><span class="n" style="color: #333;">wig</span><span class="p">,</span><span class="n" style="color: #333;">W</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">  <span class="n" style="color: #333;">runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">  <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">wig</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">  <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="p">:</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">wig</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="python">      <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">      <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">wig</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="python">      <span class="n" style="color: #333;">runs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">      <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">  <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">W</span><span class="p">:</span> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">wig</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">      <span class="nb" style="color: #0086b3;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runs</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">      <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">wig</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">:</span><span class="nb" style="color: #0086b3;">next</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">counts</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(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="LC34" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(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="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_counts</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">,</span><span class="n" style="color: #333;">counts</span><span class="p">,</span><span class="n" style="color: #333;">gene</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">  <span class="n" style="color: #333;">cnts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(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="LC37" class="line" lang="python">  <span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">'start'</span><span class="p">],</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">'end'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(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="LC38" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">co</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">end</span><span class="p">:</span> <span class="n" style="color: #333;">cnts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cnts</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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

<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sample_counts</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span><span class="n" style="color: #333;">size</span><span class="p">,</span><span class="n" style="color: #333;">times</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="python">  <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC44" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">times</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">    <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">random</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span><span class="n" style="color: #333;">size</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># without replacement</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samples</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">###################################</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(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="LC51" class="line" lang="python">  <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"usage: python fitness_defect.py <comma_separated_list_of_wig_files> <prot_table>"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(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="LC52" class="line" lang="python">  <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(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="LC53" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(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="LC54" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"# command: python"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">x</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="n" style="color: #333;">coords</span><span class="p">,</span><span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_wig</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pytransit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tnseq_tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_genes</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="n" style="color: #333;">noness</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remove_essential_regions</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># run length</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(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="LC62" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'# sites: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, noness: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">),</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">noness</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="n" style="color: #333;">noness_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">((</span><span class="n" style="color: #333;">noness</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="n" style="color: #333;">noness_NZvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">noness_arr</span><span class="p">[</span><span class="n" style="color: #333;">noness_arr</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(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="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'# noness: zeros=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, NZmean=</span><span class="si" style="color: #d14;">%0.1</span><span class="s" style="color: #d14;">f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">noness_NZvals</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span><span class="p">,</span><span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">noness_NZvals</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(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="LC66" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(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="LC68" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">  <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">'rv'</span><span class="p">],</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">'gene'</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">  <span class="n" style="color: #333;">cnts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_counts</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">,</span><span class="n" style="color: #333;">counts</span><span class="p">,</span><span class="n" style="color: #333;">gene</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">  <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cnts</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">  <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">  <span class="n" style="color: #333;">nonzeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">cnts</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonzero</span><span class="p">(</span><span class="n" style="color: #333;">cnts</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(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="LC76" class="line" lang="python">  <span class="n" style="color: #333;">zeros</span><span class="p">,</span><span class="n" style="color: #333;">NZmean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nonzeros</span><span class="p">),</span><span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">nonzeros</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nonzeros</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">  <span class="n" style="color: #333;">sat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nonzeros</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">  <span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">cnts</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">  <span class="n" style="color: #333;">mn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tot</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">  <span class="c1" style="color: #998; font-style: italic;"># determine p-value by comparing to sum of counts for random draws of sites from noness</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python">  <span class="n" style="color: #333;">N</span><span class="p">,</span><span class="n" style="color: #333;">alpha</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span><span class="mf" style="color: #099;">0.05</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">  <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cache</span><span class="p">:</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cache</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">  <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">    <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_counts</span><span class="p">(</span><span class="n" style="color: #333;">noness</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">N</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">    <span class="n" style="color: #333;">cache</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">  <span class="n" style="color: #333;">samplesums</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">lst</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lst</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sample</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(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="LC88" class="line" lang="python">  <span class="n" style="color: #333;">meansum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">samplesums</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="python">  <span class="n" style="color: #333;">PC</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="c1" style="color: #998; font-style: italic;"># pseudo-counts</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(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="LC90" class="line" lang="python">  <span class="n" style="color: #333;">rel</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">cnts</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">meansum</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python">  <span class="n" style="color: #333;">LFC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">rel</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python">  <span class="n" style="color: #333;">lesser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">tot</span><span class="p">,</span><span class="n" style="color: #333;">samplesums</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="python">  <span class="n" style="color: #333;">greater</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">tot</span><span class="p">,</span><span class="n" style="color: #333;">samplesums</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="python">  <span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">lesser</span><span class="p">,</span><span class="n" style="color: #333;">greater</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">N</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(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="LC97" class="line" lang="python">  <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"rv gene start end strand"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(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="LC98" class="line" lang="python">  <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cnts</span><span class="p">),</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tot</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.1</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">mn</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.3</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sat</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nonzeros</span><span class="p">),</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.1</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">NZmean</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python">  <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">meansum</span><span class="p">),</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.3</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">rel</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.3</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">LFC</span><span class="p">,</span><span class="n" style="color: #333;">pval</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python">  <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python">  <span class="c1" style="color: #998; font-style: italic;">#if gene['rv']=='Rv0020c': break</span></span>

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

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="n" style="color: #333;">pvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="n" style="color: #333;">qvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">fdrcorrection</span><span class="p">(</span><span class="n" style="color: #333;">pvals</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.6</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span><span class="n" style="color: #333;">qvals</span><span class="p">)]</span></span>

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

</pre>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"ORF gene start end strand TAs sum mean sat NZsites NZmean expec_sum FC LFC pval qval"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">())</span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">vals</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python">  <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vals</span><span class="p">])</span></span></pre>

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<br>

</li>

<li id="176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4"><strong>src/pytransit/__init__.py</strong></a>

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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;">"v3.0.<span class="idiff left right">1</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;">"v3.0.<span class="idiff left right">2</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/20d19355d501e251533c1e6e708100581caffe85#8f7b871a787b5d5c5b3a11bed95337c59a510906"><strong>src/pytransit/analysis/gi.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="580" 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">@@ -580,10 +580,19 @@ class GIMethod(base.QuadConditionMethod):</td>

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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transit_tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cleanargs</span><span class="p">(</span><span class="n" style="color: #333;">rawargs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="582" 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">

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># ctrl-vs-exp = condition 1-vs-2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># originally, MAD defined order of CL args this way: strA/cond1, strB/cond1, strA/cond2, strB/cond</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#ctrldataA = args[0].split(",")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#ctrldataB = args[1].split(",")</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(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="587" style="width: 35px; color: rgba(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="LC587" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#expdataA = args[2].split(",")</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(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="588" style="width: 35px; color: rgba(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="LC588" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#expdataB = args[3].split(",")</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="589" style="width: 35px; color: rgba(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="LC589" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TRI changed order of args this way: strA/cond1, strA/cond2, strB/cond1, strB/cond</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="591" 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="LC591" class="line" lang="python">        <span class="n" style="color: #333;">ctrldataA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="592" style="width: 35px; color: rgba(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="LC584" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">ctrldataB</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

585

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<td class="diff-line-num new_line old" data-linenumber="592" style="width: 35px; color: rgba(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="LC585" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">expdataA</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">expdataA</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="593" style="width: 35px; color: rgba(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="LC593" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">ctrldataB</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="594" 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="LC594" class="line" lang="python">        <span class="n" style="color: #333;">expdataB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="587" style="width: 35px; color: rgba(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="595" style="width: 35px; color: rgba(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="LC595" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="587" 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="596" 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="LC596" class="line" lang="python">        <span class="n" style="color: #333;">annotationPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="588" 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">

588

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<td class="diff-line-num new_line" data-linenumber="597" 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="LC597" class="line" lang="python">        <span class="n" style="color: #333;">output_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</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="589" 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">

589

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<td class="diff-line-num new_line" data-linenumber="598" 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="LC598" class="line" lang="python">        <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">output_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="633" 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="642" 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">@@ -633,7 +642,6 @@ class GIMethod(base.QuadConditionMethod):</td>

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<td class="diff-line-num old_line" data-linenumber="633" 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">

633

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<td class="diff-line-num new_line" data-linenumber="642" 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">

642

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python">        <span class="n" style="color: #333;">Na2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expdataA</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="634" 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="643" 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="LC643" class="line" lang="python">        <span class="n" style="color: #333;">Nb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expdataB</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="635" 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">

635

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<td class="diff-line-num new_line" data-linenumber="644" 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">

644

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="636" style="width: 35px; color: rgba(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="645" style="width: 35px; color: rgba(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="LC636" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="637" 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">

637

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<td class="diff-line-num new_line" data-linenumber="645" 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="LC645" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Get data</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="638" 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="646" 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">

646

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Getting Data"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="639" 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">

639

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<td class="diff-line-num new_line" data-linenumber="647" 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">

647

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transit_tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_validated_data</span><span class="p">(</span><span class="n" style="color: #333;">wiglist</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="893" 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="901" 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">@@ -893,7 +901,13 @@ class GIMethod(base.QuadConditionMethod):</td>

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<td class="diff-line-num old_line" data-linenumber="893" 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">

893

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<td class="diff-line-num new_line" data-linenumber="901" 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">

901

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<pre style="margin: 0;"> <span id="LC901" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="894" 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">

894

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<td class="diff-line-num new_line" data-linenumber="902" 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">

902

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<pre style="margin: 0;"> <span id="LC902" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="895" 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">

895

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<td class="diff-line-num new_line" data-linenumber="903" 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">

903

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<pre style="margin: 0;"> <span id="LC903" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

896

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<pre style="margin: 0;">-<span id="LC896" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""python </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s GI <comma-separated .wig control files condition A> <comma-separated .wig control files condition B> <comma-separated .wig experimental files condition A> <comma-separated .wig experimental files condition B> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span></span>

</pre>

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</td>

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904

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<pre style="margin: 0;">+<span id="LC904" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#return """python %s GI <comma-separated .wig control files condition A> <comma-separated .wig control files condition B> <comma-separated .wig experimental files condition A> <comma-separated .wig experimental files condition B> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

905

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<pre style="margin: 0;">+<span id="LC905" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""python </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s GI <wigs_for_strA_cond1> <wigs_for_strA_cond2> <wigs_for_strB_cond1> <wigs_for_strB_cond2> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(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="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

906

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<pre style="margin: 0;">+<span id="LC906" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(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="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

907

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<pre style="margin: 0;">+<span id="LC907" class="line" lang="python"><span class="s" style="color: #d14;">        GI performs a comparison among 4 groups of datasets, strain A and B assessed in conditions 1 and 2 (e.g. control vs treatment).</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

908

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<pre style="margin: 0;">+<span id="LC908" class="line" lang="python"><span class="s" style="color: #d14;">        It looks for interactions where the response to the treatment (i.e. effect on insertion counts) depends on the strain (output variable: delta_LFC).</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(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="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

909

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<pre style="margin: 0;">+<span id="LC909" class="line" lang="python"><span class="s" style="color: #d14;">        Provide replicates in each group as a comma-separated list of wig files.</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

910

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<pre style="margin: 0;">+<span id="LC910" class="line" lang="python"><span class="s" style="color: #d14;">        Significant interactions are those with "HDI outside ROPE?"=TRUE, and all genes are sorted by significance using BFDR."</span></span>

</pre>

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897

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<td class="diff-line-num new_line" data-linenumber="911" 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">

911

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<pre style="margin: 0;"> <span id="LC911" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="898" 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">

898

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<td class="diff-line-num new_line" data-linenumber="912" 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">

912

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<pre style="margin: 0;"> <span id="LC912" class="line" lang="python"><span class="s" style="color: #d14;">        Optional Arguments:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="899" 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">

899

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<td class="diff-line-num new_line" data-linenumber="913" 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">

913

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<pre style="margin: 0;"> <span id="LC913" class="line" lang="python"><span class="s" style="color: #d14;">        -s <integer>    :=  Number of samples. Default: -s 10000</span></span>

</pre>

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<br>

</li>

<li id="46073ef784cdc338b0714d64bb6fd29c8fbdaf90">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#46073ef784cdc338b0714d64bb6fd29c8fbdaf90"><strong>src/pytransit/analysis/resampling.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="641" 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="641" 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">@@ -641,8 +641,8 @@ class ResamplingMethod(base.DualConditionMethod):</td>

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641

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"><span class="s" style="color: #d14;">        -pc             :=  Pseudocounts to be added at each site.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"><span class="s" style="color: #d14;">        -l              :=  Perform LOESS Correction; Helps remove possible genomic position bias.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="643" 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="LC643" class="line" lang="python"><span class="s" style="color: #d14;">                            Default: Turned Off.</span></span>

</pre>

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644

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<td class="diff-line-num new_line old" data-linenumber="644" style="width: 35px; color: rgba(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="LC644" class="line" lang="python"><span class="s" style="color: #d14;">        -iN <<span class="idiff left right">float></span>     :=  Ignore TAs occuring within given percentage (as integer) of the N terminus. Default: -iN 0</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

645

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<td class="diff-line-num new_line old" data-linenumber="644" style="width: 35px; color: rgba(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="LC645" class="line" lang="python"><span class="s" style="color: #d14;">        -iC <<span class="idiff left right">float></span>     :=  Ignore TAs occuring within given percentage (as integer) of the C terminus. Default: -iC 0</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="644" style="width: 35px; color: rgba(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="LC644" class="line" lang="python"><span class="s" style="color: #d14;">        -iN <<span class="idiff left right">int>  </span>     :=  Ignore TAs occuring within given percentage (as integer) of the N terminus. Default: -iN 0</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

645

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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"><span class="s" style="color: #d14;">        -iC <<span class="idiff left right">int>  </span>     :=  Ignore TAs occuring within given percentage (as integer) of the C terminus. Default: -iC 0</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"><span class="s" style="color: #d14;">        --ctrl_lib      :=  String of letters representing library of control files in order</span></span>

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"><span class="s" style="color: #d14;">                            e.g. 'AABB'. Default empty. Letters used must also be used in --exp_lib</span></span>

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python"><span class="s" style="color: #d14;">                            If non-empty, resampling will limit permutations to within-libraries.</span></span>

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</li>

<li id="07ca99dc668f43ea2451861342e18d287151cf0c">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#07ca99dc668f43ea2451861342e18d287151cf0c"><strong>src/pytransit/analysis/zinb.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">@@ -248,7 +248,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"><span class="s" style="color: #d14;">              # filter out genes that have low saturation across all conditions, since pscl sometimes does not fit params well (resulting in large negative intercepts and high std errors)</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;">              NZpercs = aggregate(melted$cnt,by=list(melted$cond),FUN=function(x) { sum(x>0)/length(x) })</span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"><span class="s" style="color: #d14;">              if (max(NZpercs$x)<<span class="idiff left right">=0.15) { return(c(pval=1,status="low saturation (near-essential) across all conditions,</span> not analyzed")) }</span></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"><span class="s" style="color: #d14;">              if (max(NZpercs$x)<<span class="idiff left">0.15) { return(c(pval=1,status="low saturation (<15</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">) across all conditions (pan-growth-defect) -</span> not analyzed")) }</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"><span class="s" style="color: #d14;">              sums = aggregate(melted$cnt,by=list(melted$cond),FUN=sum)</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"><span class="s" style="color: #d14;">              # to avoid model failing due to singular condition, add fake counts of 1 to all conds if any cond is all 0s</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -271,7 +271,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;">                    mod = zeroinfl(as.formula(zinbMod1),data=melted,dist="negbin")</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"><span class="s" style="color: #d14;">                    coeffs = summary(mod)$coefficients</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;">                    # [,1] is col of parms, [,2] is col of stderrs, assume Intercept is always first</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"><span class="s" style="color: #d14;">                    if (coeffs$count[,2][1]>0.5) { status = 'warning: high stderr on Intercept for mod1' }</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"><span class="s" style="color: #d14;">                    <span class="idiff left right">#</span>if (coeffs$count[,2][1]>0.5) { status = 'warning: high stderr on Intercept for mod1' }</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;">                    mod</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;">                  } else {</span></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;">                    f1 = nbMod1</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="311" 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="311" 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">@@ -311,8 +311,9 @@ class ZinbMethod(base.MultiConditionMethod):</td>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;">              }</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;">              if (is.null(mod1) | is.null(mod0)) { return (c(1, paste0("Model Error. ", status))) }</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;">              if ((minCount == 0) && (sum(is.na(coef(summary(mod1))$count[,4]))>0)) { return(c(1, "Has Coefs, <span class="idiff left right">pvals are NAs</span>")) } # rare failure mode - has coefs, but pvals are NA</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;">              if ((minCount == 0) && (sum(is.na(coef(summary(mod1))$count[,4]))>0)) { return(c(1, "Has Coefs, <span class="idiff left right">but Pvals are NAs (model failure)</span>")) } # rare failure mode - has coefs, but pvals are NA</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;">              df1 = attr(logLik(mod1),"df"); df0 = attr(logLik(mod0),"df") # should be (2*ngroups+1)-3</span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;">              if (DEBUG) print(sprintf("delta_log_likelihood=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f",logLik(mod1)-logLik(mod0)))</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;">              pval = pchisq(2*(logLik(mod1)-logLik(mod0)),df=df1-df0,lower.tail=F) # alternatively, could use lrtest()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;">              # this gives same answer, but I would need to extract the Pvalue...</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;">              #require(lmtest)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="394" 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="395" 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">@@ -394,8 +395,12 @@ class ZinbMethod(base.MultiConditionMethod):</td>

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transit_error</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot find gene: {0}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">GENE</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python">                    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="397" style="width: 35px; color: rgba(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="LC398" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">DEBUG</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python">               <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"======================================================================"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python">               <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"rv"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="397" style="width: 35px; color: rgba(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="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="397" 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="402" 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="LC402" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">RvSiteindexesMap</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

398

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<td class="diff-line-num new_line old" data-linenumber="403" style="width: 35px; color: rgba(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="LC398" class="line" lang="python">                <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"TA sites <= 1"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="399" style="width: 35px; color: rgba(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="403" style="width: 35px; color: rgba(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="LC403" class="line" lang="python">                <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"TA sites <= 1<span class="idiff left right">, not analyzed</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" 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="404" 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="LC404" class="line" lang="python">                <span class="n" style="color: #333;">pvals</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="405" 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="LC405" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="401" 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="406" 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="LC406" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># For winsorization</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="411" 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="416" 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">@@ -411,7 +416,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>

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<td class="diff-line-num old_line" data-linenumber="411" 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="LC416" class="line" lang="python">                           <span class="n" style="color: #333;">norm_data</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="412" 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="417" 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="LC417" class="line" lang="python">                           <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">covariates</span><span class="p">,</span> <span class="n" style="color: #333;">interactions</span><span class="p">,</span> <span class="n" style="color: #333;">NZMeanByRep</span><span class="p">,</span> <span class="n" style="color: #333;">LogZPercByRep</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="418" 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="LC418" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">readCounts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="419" style="width: 35px; color: rgba(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="LC414" class="line" lang="python">                    <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">No counts in all conditions</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="415" style="width: 35px; color: rgba(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="419" style="width: 35px; color: rgba(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="LC419" class="line" lang="python">                    <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">pan-essential (no counts in all conditions) - not analyzed</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="415" 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="420" 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="LC420" class="line" lang="python">                    <span class="n" style="color: #333;">pvals</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="421" 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="LC421" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="417" 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="422" 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="LC422" class="line" lang="python">                    <span class="n" style="color: #333;">df_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="525" 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="530" 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">@@ -525,8 +530,11 @@ class ZinbMethod(base.MultiConditionMethod):</td>

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<td class="diff-line-num old_line" data-linenumber="525" 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="530" 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="LC530" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Adding File: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">headersStatGroupNames</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">lfcNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"LFC"</span><span class="p">]</span> </span>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">lfcNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="s" style="color: #d14;">"LFC_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">v</span><span class="p">,</span><span class="n" style="color: #333;">headersStatGroupNames</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">        <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"Rv Gene TAs"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span></span>

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python">                <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="s" style="color: #d14;">"Mean_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">headersStatGroupNames</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span></span>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python">                <span class="n" style="color: #333;">lfcNames</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python">                <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="s" style="color: #d14;">"NZmean_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">headersStatGroupNames</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span></span>

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python">                <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="s" style="color: #d14;">"NZperc_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">headersStatGroupNames</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span></span>

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python">                <span class="s" style="color: #d14;">"pval padj"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">"status"</span><span class="p">])</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="535" 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="543" 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">@@ -535,9 +543,16 @@ class ZinbMethod(base.MultiConditionMethod):</td>

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python">        <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">head</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">EOL</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="545" 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="LC545" class="line" lang="python">            <span class="n" style="color: #333;">Rv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"rv"</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python">            <span class="n" style="color: #333;">means</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python">            <span class="n" style="color: #333;">PC</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="548" style="width: 35px; color: rgba(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="LC548" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">LFCs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">((</span><span class="n" style="color: #333;">means</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">),</span><span class="mi" style="color: #099;">2</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="550" style="width: 35px; color: rgba(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="LC550" class="line" lang="python">              <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="551" style="width: 35px; color: rgba(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="LC551" class="line" lang="python">              <span class="n" style="color: #333;">LFCs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">((</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">),</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">means</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="552" 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="LC552" class="line" lang="python">            <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">([</span><span class="n" style="color: #333;">Rv</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">RvSiteindexesMap</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]))]</span> <span class="o" style="font-weight: 600;">+</span></span>

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<td class="diff-line-num new_line old" data-linenumber="553" style="width: 35px; color: rgba(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="LC539" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.2</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>

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<td class="diff-line-num new_line old" data-linenumber="553" style="width: 35px; color: rgba(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="LC540" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.2</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'nz_mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.1</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.3</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">LFCs</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

555

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.1</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'nz_mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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541

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<td class="diff-line-num new_line" data-linenumber="556" 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">

556

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%0.2</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'nz_perc'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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542

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">pvals</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">],</span> <span class="n" style="color: #333;">qvals</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]]])</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">run_status</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]]</span></span>

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543

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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python">            <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">EOL</span><span class="p">)</span></span>

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<li id="e4c47efb9db43431093096e67f5aab587b257ff4">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#e4c47efb9db43431093096e67f5aab587b257ff4"><strong>src/pytransit/doc/source/transit_methods.rst</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">@@ -534,7 +534,7 @@ parameters are available for the method:</td>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="plaintext">   which are likely not significant. This dramatically speeds up the</span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="plaintext">   computation at the cost of less accurate estimates for those genes</span>

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="plaintext">   that terminate early (i.e. deemed not significant). This option is</span>

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<pre style="margin: 0;">-<span id="LC537" class="line" lang="plaintext">   OFF by default.</span>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext">   OFF by default.<span class="idiff left right"> (see Notes below)</span></span>

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<pre style="margin: 0;"> <span id="LC538" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="plaintext">-  **Include Zeros:** Select to include  sites that are zero. This is the</span>

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="plaintext">   preferred behavior, however, unselecting this (thus ignoring sites that)</span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="547" 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">@@ -547,10 +547,37 @@ parameters are available for the method:</td>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="plaintext">   as real differences. See the :ref:`Normalization <normalization>` section for a description</span>

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="plaintext">   of normalization method available in TRANSIT.</span>

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC550" class="line" lang="plaintext">-  **--ctrl_lib, --exp_lib** These are for doing resampling with datasets from multiple libraries, see below.</span>

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext">-  **--ctrl_lib, --exp_lib:** These are for doing resampling with datasets from multiple libraries, see below.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext">-  **-iN, -iC:** Trimming of TA sites near N- and C-terminus.</span>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext">   The default for trimming TA sites in the termini of ORFs is 0.</span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext">   However, TA sites in the stop codon (e.g. TAG) are automatically excluded.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext">   Trimming is specified as a percentage (as an integer), so, for example,</span>

</pre>

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556

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext">   if you want to trim TA sites within 5% of the termini, you would </span>

</pre>

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557

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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext">   add the flags '-iN 5 -iC 5' (not 0.05).</span>

</pre>

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558

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext"></span>

</pre>

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559

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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext">-  **-pc**: Pseudocounts for resampling.  By default, pseudocounts are not used.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext">   However, if you set '-pc 5', for example, it will add an insertion count of 5</span>

</pre>

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561

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext">   at a "fake" site in each condition, which can help smooth out the impact of noise</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

562

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext">   (e.g. large apprarent log-fold-changes (LFCs) due to just a few small counts).</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

563

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext">   Note that, when calculating LFCs, if either the numerator or denominator is 0,</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="564" style="width: 35px; color: rgba(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="LC564" class="line" lang="plaintext">   a 1 is automatically added to both to prevent numerically undefined results.</span>

</pre>

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565

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext"></span>

</pre>

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551

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566

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="plaintext"></span>

</pre>

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552

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567

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="plaintext">|</span>

</pre>

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553

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568

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<pre style="margin: 0;"> <span id="LC568" class="line" lang="plaintext"></span>

</pre>

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569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext">Notes</span>

</pre>

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570

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext">~~~~~</span>

</pre>

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571

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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="554" style="width: 35px; color: rgba(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="572" style="width: 35px; color: rgba(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="LC572" class="line" lang="plaintext">I recommend using -a (adaptive resampling). It runs much faster, and the p-values</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="573" style="width: 35px; color: rgba(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="LC573" class="line" lang="plaintext">will be very close to a full non-adaptive run (all 10,000 samples).</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

574

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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext"></span>

</pre>

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575

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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext">Occasionally, people ask if resampling can be done on intergenic regions as well.</span>

</pre>

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576

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext">It could be done pretty easily (for example by making a prot_table with coordinates</span>

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577

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext">for the regions between genes).  But it is usually not worthwhile, because most</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext">intergenic regions are small (<100 bp) contain very few TA sites (often 0-2),</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext">making it difficult to make confident calls on essentiality.</span>

</pre>

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580

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"></span>

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554

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581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="plaintext"></span>

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555

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<td class="diff-line-num new_line" data-linenumber="582" 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">

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="plaintext">Doing resampling with a combined_wig file</span>

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556

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583

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="752" 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="779" 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">@@ -752,19 +779,33 @@ that imply a genetic interaction.</td>

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752

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779

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<pre style="margin: 0;"> <span id="LC779" class="line" lang="plaintext">How does it work?</span>

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753

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<pre style="margin: 0;"> <span id="LC780" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~</span>

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754

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781

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<pre style="margin: 0;"> <span id="LC781" class="line" lang="plaintext"></span>

</pre>

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755

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<pre style="margin: 0;">-<span id="LC755" class="line" lang="plaintext">| For a formal description of how this method works, see our paper [DeJesus20170NAR]_:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC782" class="line" lang="plaintext">GI performs a comparison among 4 groups of datasets, strain A and B assessed in conditions 1 and 2 (e.g. control vs treatment).</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="783" style="width: 35px; color: rgba(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="LC783" class="line" lang="plaintext">It looks for interactions where the response to the treatment (i.e. effect on insertion counts) depends on the strain.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

784

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<pre style="margin: 0;">+<span id="LC784" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

785

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<pre style="margin: 0;">+<span id="LC785" class="line" lang="plaintext">If you think of the effect of treatment as a log-fold-change (e.g. of</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

786

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<pre style="margin: 0;">+<span id="LC786" class="line" lang="plaintext">the insert counts between control and treatment in strain A), which is</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

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<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext">like a "slope", then the interacting genes are those that exhibit a difference</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

788

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<pre style="margin: 0;">+<span id="LC788" class="line" lang="plaintext">in the effect of the treatment between the strains, and hence a difference in the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

789

</td>

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<pre style="margin: 0;">+<span id="LC789" class="line" lang="plaintext">slopes between strain A and B (represented by 'delta_LFC' in the output file).</span>

</pre>

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</tr>

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<td class="diff-line-num new old_line" data-linenumber="756" style="width: 35px; color: rgba(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="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

790

</td>

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

<pre style="margin: 0;">+<span id="LC790" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="756" style="width: 35px; color: rgba(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="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

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<pre style="margin: 0;">+<span id="LC791" class="line" lang="plaintext">| For a formal description of how this method works, see our paper [DeJesus2017NAR]_:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="756" 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">

756

</td>

<td class="diff-line-num new_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

</td>

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

<pre style="margin: 0;"> <span id="LC792" class="line" lang="plaintext">|</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="757" 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">

757

</td>

<td class="diff-line-num new_line" data-linenumber="793" 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">

793

</td>

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

<pre style="margin: 0;"> <span id="LC793" class="line" lang="plaintext">|  DeJesus, M.A., Nambi, S., Smith, C.M., Baker, R.E., Sassetti, C.M., Ioerger, T.R. `Statistical analysis of genetic interactions in Tn-Seq data. <https://www.ncbi.nlm.nih.gov/pubmed/28334803>`_ *Nucleic Acids Research.* 2017. 45(11):e93. doi: 10.1093/nar/gkx128.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="758" 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">

758

</td>

<td class="diff-line-num new_line" data-linenumber="794" 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">

794

</td>

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

<pre style="margin: 0;"> <span id="LC794" class="line" lang="plaintext"></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="759" style="width: 35px; color: rgba(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="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

795

</td>

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

<pre style="margin: 0;">+<span id="LC795" class="line" lang="plaintext"></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="759" style="width: 35px; color: rgba(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="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

796

</td>

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

<pre style="margin: 0;">+<span id="LC796" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="759" 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">

759

</td>

<td class="diff-line-num new_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

</td>

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

<pre style="margin: 0;"> <span id="LC797" class="line" lang="plaintext">|</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="760" 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">

760

</td>

<td class="diff-line-num new_line" data-linenumber="798" 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">

798

</td>

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

<pre style="margin: 0;"> <span id="LC798" class="line" lang="plaintext"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="761" 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">

761

</td>

<td class="diff-line-num new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

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

<pre style="margin: 0;"> <span id="LC799" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

762

</td>

<td class="diff-line-num new_line old" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC762" class="line" lang="plaintext"><span class="idiff left right">Exampl</span>e</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

763

</td>

<td class="diff-line-num new_line old" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC763" class="line" lang="plaintext">~~~~~<span class="idiff left right">~~</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="764" style="width: 35px; color: rgba(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="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

800

</td>

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

<pre style="margin: 0;">+<span id="LC800" class="line" lang="plaintext"><span class="idiff left right">Usag</span>e</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="764" style="width: 35px; color: rgba(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="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

</td>

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

<pre style="margin: 0;">+<span id="LC801" class="line" lang="plaintext">~~~~~</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="764" 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">

764

</td>

<td class="diff-line-num new_line" data-linenumber="802" 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">

802

</td>

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

<pre style="margin: 0;"> <span id="LC802" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="765" 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">

765

</td>

<td class="diff-line-num new_line" data-linenumber="803" 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">

803

</td>

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

<pre style="margin: 0;"> <span id="LC803" class="line" lang="plaintext">::</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="766" 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">

766

</td>

<td class="diff-line-num new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

</td>

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

<pre style="margin: 0;"> <span id="LC804" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

767

</td>

<td class="diff-line-num new_line old" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC767" class="line" lang="plaintext">  python transit.py GI <comma-separated .wig control files condition A> <comma-separated .wig control files condition B> <comma-separated .wig experimental files condition A> <comma-separated .wig experimental files condition B> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="768" style="width: 35px; color: rgba(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="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

805

</td>

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

<pre style="margin: 0;">+<span id="LC805" class="line" lang="plaintext">  python transit.py GI <wigs_for_strA_cond1> <wigs_for_strA_cond2> <wigs_for_strB_cond1> <wigs_for_strB_cond2> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="768" style="width: 35px; color: rgba(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="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

806

</td>

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

<pre style="margin: 0;">+<span id="LC806" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="768" style="width: 35px; color: rgba(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="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

807

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="plaintext">        Provide replicates in each group as a comma-separated list of wig files.</span>

</pre>

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808

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<pre style="margin: 0;">+<span id="LC808" class="line" lang="plaintext"></span>

</pre>

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768

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<td class="diff-line-num new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

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<pre style="margin: 0;"> <span id="LC809" class="line" lang="plaintext">        Optional Arguments:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

769

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<td class="diff-line-num new_line" data-linenumber="810" 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">

810

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<pre style="margin: 0;"> <span id="LC810" class="line" lang="plaintext">        -s <integer>    :=  Number of samples. Default: -s 10000</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="770" 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">

770

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<td class="diff-line-num new_line" data-linenumber="811" 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">

811

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="plaintext">        --rope <float>  :=  Region of Practical Equivalence. Area around 0 (i.e. 0 +/- ROPE) that is NOT of interest. Can be thought of similar to the area of the null-hypothesis. Default: --rope 0.5</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="776" 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="817" 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">@@ -776,6 +817,19 @@ Example</td>

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776

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<td class="diff-line-num new_line" data-linenumber="817" 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">

817

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

<pre style="margin: 0;"> <span id="LC817" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="777" 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">

777

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<td class="diff-line-num new_line" data-linenumber="818" 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">

818

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<pre style="margin: 0;"> <span id="LC818" class="line" lang="plaintext">You can think of 'control' and 'experimental' samples as 'untreated' vs. 'treated'.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="778" 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">

778

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<td class="diff-line-num new_line" data-linenumber="819" 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">

819

</td>

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

<pre style="margin: 0;"> <span id="LC819" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

820

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<pre style="margin: 0;">+<span id="LC820" class="line" lang="plaintext">Example</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

821

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<pre style="margin: 0;">+<span id="LC821" class="line" lang="plaintext">~~~~~~~</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

822

</td>

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

<pre style="margin: 0;">+<span id="LC822" class="line" lang="plaintext"></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="779" style="width: 35px; color: rgba(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="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

823

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<pre style="margin: 0;">+<span id="LC823" class="line" lang="plaintext">In this example, the effect of a knockout of SigB is being evaluated for its effect on tolerance of isoniazid.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

824

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<pre style="margin: 0;">+<span id="LC824" class="line" lang="plaintext">Some genes may become more essential (or less) in the presence of INH in the wild-type strain.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

825

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<pre style="margin: 0;">+<span id="LC825" class="line" lang="plaintext">The genes implied to interact with SigB are those whose response to INH changes in the knock-out strain compared to the wild-type.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

826

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<pre style="margin: 0;">+<span id="LC826" class="line" lang="plaintext">Note there are 2 replicates in each of the 4 groups of datasets.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

827

</td>

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

<pre style="margin: 0;">+<span id="LC827" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

828

</td>

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<pre style="margin: 0;">+<span id="LC828" class="line" lang="plaintext">::</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

829

</td>

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<pre style="margin: 0;">+<span id="LC829" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

830

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<pre style="margin: 0;">+<span id="LC830" class="line" lang="plaintext">  python transit/src/transit.py GI WT_untreated1.wig,WT_untreated2.wig WT_INH_1.wig,WT_INH_2.wig delta_SigB_untreated1.wig,delta_SigB_untreated2.wig delta_SigB_INH_1.wig,delta_SigB_INH_2.wig mc2_155_tamu.prot_table GI_delta_SigB_INH.txt</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

831

</td>

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

<pre style="margin: 0;">+<span id="LC831" class="line" lang="plaintext"></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

832

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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="LC832" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="779" 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">

779

</td>

<td class="diff-line-num new_line" data-linenumber="833" 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">

833

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

<pre style="margin: 0;"> <span id="LC833" class="line" lang="plaintext">Parameters</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="780" 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">

780

</td>

<td class="diff-line-num new_line" data-linenumber="834" 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">

834

</td>

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

<pre style="margin: 0;"> <span id="LC834" class="line" lang="plaintext">~~~~~~~~~~</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="781" 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">

781

</td>

<td class="diff-line-num new_line" data-linenumber="835" 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">

835

</td>

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

<pre style="margin: 0;"> <span id="LC835" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="858" 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="912" 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">@@ -858,6 +912,11 @@ typical threshold for conditional essentiality on is q-value < 0.05.</td>

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<td class="diff-line-num old_line" data-linenumber="858" 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">

858

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<td class="diff-line-num new_line" data-linenumber="912" 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">

912

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

<pre style="margin: 0;"> <span id="LC912" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="859" 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">

859

</td>

<td class="diff-line-num new_line" data-linenumber="913" 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">

913

</td>

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

<pre style="margin: 0;"> <span id="LC913" class="line" lang="plaintext">|</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="860" 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">

860

</td>

<td class="diff-line-num new_line" data-linenumber="914" 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">

914

</td>

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

<pre style="margin: 0;"> <span id="LC914" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(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="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

915

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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="LC915" class="line" lang="plaintext">Significant interactions are those with "HDI outside ROPE?"=TRUE.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(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="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

916

</td>

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

<pre style="margin: 0;">+<span id="LC916" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(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="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

917

</td>

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

<pre style="margin: 0;">+<span id="LC917" class="line" lang="plaintext">All genes are sorted by significance using BFDR.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(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="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

918

</td>

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

<pre style="margin: 0;">+<span id="LC918" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="861" style="width: 35px; color: rgba(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="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

919

</td>

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

<pre style="margin: 0;">+<span id="LC919" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="861" 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">

861

</td>

<td class="diff-line-num new_line" data-linenumber="920" 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">

920

</td>

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

<pre style="margin: 0;"> <span id="LC920" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="862" 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">

862

</td>

<td class="diff-line-num new_line" data-linenumber="921" 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">

921

</td>

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<pre style="margin: 0;"> <span id="LC921" class="line" lang="plaintext">.. rst-class:: transit_sectionend</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="863" 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">

863

</td>

<td class="diff-line-num new_line" data-linenumber="922" 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">

922

</td>

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

<pre style="margin: 0;"> <span id="LC922" class="line" lang="plaintext">----</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1010" 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="1069" 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">@@ -1010,7 +1069,9 @@ to be installed on your system.  See :ref:`Installation Instructions <install-zi</td>

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<td class="diff-line-num old_line" data-linenumber="1010" 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">

1010

</td>

<td class="diff-line-num new_line" data-linenumber="1069" 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">

1069

</td>

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

<pre style="margin: 0;"> <span id="LC1069" class="line" lang="plaintext">How does it work?</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1011" 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">

1011

</td>

<td class="diff-line-num new_line" data-linenumber="1070" 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">

1070

</td>

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

<pre style="margin: 0;"> <span id="LC1070" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1012" 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">

1012

</td>

<td class="diff-line-num new_line" data-linenumber="1071" 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">

1071

</td>

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

<pre style="margin: 0;"> <span id="LC1071" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1013

</td>

<td class="diff-line-num new_line old" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1013" class="line" lang="plaintext">| For a formal description of how this method works, see our `paper on bioRxiv <https://www.biorxiv.org/content/10.1101/590281v1>`_.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1072

</td>

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

<pre style="margin: 0;">+<span id="LC1072" class="line" lang="plaintext">| For a formal description of how this method works, see our paper [ZINB]_: </span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1073

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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="plaintext">|</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1074

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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="plaintext">|  Subramaniyam S, DeJesus MA, Zaveri A, Smith CM, Baker RE, Ehrt S, Schnappinger D, Sassetti CM, Ioerger TR. (2019).  `Statistical analysis of variability in TnSeq data across conditions using Zero-Inflated Negative Binomial regression. <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3156-z>`_, *BMC Bioinformatics*. 2019 Nov 21;20(1):603. doi: 10.1186/s12859-019-3156-z.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1014" 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">

1014

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<td class="diff-line-num new_line" data-linenumber="1075" 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">

1075

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

<pre style="margin: 0;"> <span id="LC1075" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1015

</td>

<td class="diff-line-num new_line" data-linenumber="1076" 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">

1076

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

<pre style="margin: 0;"> <span id="LC1076" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1016" 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">

1016

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<td class="diff-line-num new_line" data-linenumber="1077" 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">

1077

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

<pre style="margin: 0;"> <span id="LC1077" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1019" 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="1080" 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">@@ -1019,7 +1080,7 @@ Example</td>

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<td class="diff-line-num old_line" data-linenumber="1019" 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">

1019

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<td class="diff-line-num new_line" data-linenumber="1080" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1080" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1020

</td>

<td class="diff-line-num new_line" data-linenumber="1081" 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">

1081

</td>

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

<pre style="margin: 0;"> <span id="LC1081" class="line" lang="plaintext">::</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1021" 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">

1021

</td>

<td class="diff-line-num new_line" data-linenumber="1082" 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">

1082

</td>

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

<pre style="margin: 0;"> <span id="LC1082" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1022

</td>

<td class="diff-line-num new_line old" data-linenumber="1083" style="width: 35px; color: rgba(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="LC1022" class="line" lang="plaintext">  python transit.py zinb <combined wig file> <samples_metadata file> <annotation .prot_table> <output file> [Optional Arguments]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1083

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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="plaintext">  python<span class="idiff left right">3</span> transit.py zinb <combined wig file> <samples_metadata file> <annotation .prot_table> <output file> [Optional Arguments]</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1023" 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">

1023

</td>

<td class="diff-line-num new_line" data-linenumber="1084" 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">

1084

</td>

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

<pre style="margin: 0;"> <span id="LC1084" class="line" lang="plaintext">        Optional Arguments:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1024" 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">

1024

</td>

<td class="diff-line-num new_line" data-linenumber="1085" 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">

1085

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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="plaintext">        -n <string>         :=  Normalization method. Default: -n TTR</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1025" 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">

1025

</td>

<td class="diff-line-num new_line" data-linenumber="1086" 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">

1086

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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="plaintext">        --ignore-conditions <cond1,cond2> :=  Comma separated list of conditions to ignore, for the analysis.</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1030" 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="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1030,8 +1091,7 @@ Example</td>

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<td class="diff-line-num old_line" data-linenumber="1030" 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">

1030

</td>

<td class="diff-line-num new_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1091

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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="plaintext">        --covars <covar1,covar2...>     :=  Comma separated list of covariates (in metadata file) to include, for the analysis.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1031" 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">

1031

</td>

<td class="diff-line-num new_line" data-linenumber="1092" 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">

1092

</td>

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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="plaintext">        --interactions <covar1,covar2...>     :=  Comma separated list of covariates to include, that interact with the condition for the analysis.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1032" 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">

1032

</td>

<td class="diff-line-num new_line" data-linenumber="1093" 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">

1093

</td>

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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="plaintext">        --gene <RV number or Gene name> := Run method for one gene and print model output.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1033

</td>

<td class="diff-line-num new_line old" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1033" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1034

</td>

<td class="diff-line-num new_line old" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1034" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1094

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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="plaintext">        -v              := verbose, print out the model coefficients for each gene.</span>

</pre>

</td>

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1035

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1095

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<pre style="margin: 0;"> <span id="LC1095" class="line" lang="plaintext"></span>

</pre>

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1036

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<td class="diff-line-num new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1096

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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1037" 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">

1037

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<td class="diff-line-num new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1097

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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="plaintext">.. _combined_wig:</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1295" 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="1355" 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">@@ -1295,9 +1355,15 @@ typical threshold for conditional essentiality on is q-value < 0.05.</td>

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1295

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1355

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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="plaintext">+---------------------+-----------------------------------------------------------------+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1296" 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">

1296

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<td class="diff-line-num new_line" data-linenumber="1356" 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">

1356

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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="plaintext">| TAs                 | Number of TA sites in Gene                                      |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1297" 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">

1297

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<td class="diff-line-num new_line" data-linenumber="1357" 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">

1357

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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="plaintext">+---------------------+-----------------------------------------------------------------+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1298

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<td class="diff-line-num new_line old" data-linenumber="1358" style="width: 35px; color: rgba(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="LC1298" class="line" lang="plaintext">| <Condition Mean>    | Mean read-counts for the gene, by condition                     |</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(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="LC1358" class="line" lang="plaintext">| <Mean_Condition>    | Mean read-counts for the gene, by condition                     |</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(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="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1359

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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="plaintext">+---------------------+-----------------------------------------------------------------+</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(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="1360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1360

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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="plaintext">| <LFC_Condition>     | Log-fold-change (base 2) of mean insertion count relative to    |</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1361" style="width: 35px; color: rgba(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="LC1361" class="line" lang="plaintext">|                     | mean across all conditions. Pseudo-counts of 5 are added.       |</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(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="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1362

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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="plaintext">|                     | If only 2 conditions, LFC is based on ratio of second to first. |</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(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="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1363

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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="LC1363" class="line" lang="plaintext">+---------------------+-----------------------------------------------------------------+</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(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="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1364

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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="plaintext">| <NZmean_Condition>  | Mean read-counts for the gene, by condition                     |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1299

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<td class="diff-line-num new_line" data-linenumber="1365" 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">

1365

</td>

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<pre style="margin: 0;"> <span id="LC1365" class="line" lang="plaintext">+---------------------+-----------------------------------------------------------------+</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1300

</td>

<td class="diff-line-num new_line old" data-linenumber="1366" style="width: 35px; color: rgba(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="LC1300" class="line" lang="plaintext">| <<span class="idiff left right">Condition NZMea</span>n>  | Non-zero Mean read-counts for the gene, by condition            |</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1301" style="width: 35px; color: rgba(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="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1366

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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="plaintext">| <<span class="idiff left right">NZperc_Conditio</span>n>  | Non-zero Mean read-counts for the gene, by condition            |</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1301

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<td class="diff-line-num new_line" data-linenumber="1367" 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">

1367

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

<pre style="margin: 0;"> <span id="LC1367" class="line" lang="plaintext">+---------------------+-----------------------------------------------------------------+</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="1302" 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">

1302

</td>

<td class="diff-line-num new_line" data-linenumber="1368" 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">

1368

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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="plaintext">| p-value             | P-value calculated by the ZINB test.                            |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1303

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<td class="diff-line-num new_line" data-linenumber="1369" 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">

1369

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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="plaintext">+---------------------+-----------------------------------------------------------------+</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="bf71c4ed5781c2e556f922c3622eb4c0faac245f">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#bf71c4ed5781c2e556f922c3622eb4c0faac245f"><strong>src/pytransit/doc/source/transit_overview.rst</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">@@ -149,5 +149,7 @@ Other references, including methods utilized by TRANSIT:</td>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext">.. [DeJesus2016] `DeJesus, M.A. and Ioerger, T.R. (2016). Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. Journal of Bioinformatics and Computational Biology, 14(3):1642004 <http://www.ncbi.nlm.nih.gov/pubmed/26932272>`_</span>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">.. [DeJesus20170NAR] `DeJesus, M.A., Nambi, S., Smith, C.M., Baker, R.E., Sassetti, C.M., Ioerger, T.R. Statistical analysis of genetic interactions in Tn-Seq data.  Nucleic Acids Research. 2017. 45(11):e93. doi: 10.1093/nar/gkx128. <https://www.ncbi.nlm.nih.gov/pubmed/28334803>`_</span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.. [DeJesus2017NAR] `DeJesus, M.A., Nambi, S., Smith, C.M., Baker, R.E., Sassetti, C.M., Ioerger, T.R. Statistical analysis of genetic interactions in Tn-Seq data.  Nucleic Acids Research. 2017. 45(11):e93. doi: 10.1093/nar/gkx128. <https://www.ncbi.nlm.nih.gov/pubmed/28334803>`_</span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">.. [ZINB] `Subramaniyam S, DeJesus MA, Zaveri A, Smith CM, Baker RE, Ehrt S, Schnappinger D, Sassetti CM, Ioerger TR. (2019).  Statistical analysis of variability in TnSeq data across conditions using Zero-Inflated Negative Binomial regression. *BMC Bioinformatics*. 2019 Nov 21;20(1):603. doi: 10.1186/s12859-019-3156-z. <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3156-z>`_</span>

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<li id="08b6cc113ef5013285f95a556c9c6c247be98f22">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#08b6cc113ef5013285f95a556c9c6c247be98f22"><strong>src/pytransit/export/combined_wig.py</strong></a>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">position</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="n" style="color: #333;">vals</span><span class="p">,</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">orf</span><span class="p">,</span><span class="n" style="color: #333;">rv2info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">orf</span><span class="p">,[</span><span class="s" style="color: #d14;">"-"</span><span class="p">])[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">orf</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">hash</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">position</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="p">[])])</span>   <span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Update progress</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python">            <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Running Export Method... </span><span class="si" style="color: #d14;">%5.1</span><span class="s" style="color: #d14;">f</span><span class="si" style="color: #d14;">%%</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mf" style="color: #099;">100.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">N</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">progress_update</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="mi" style="color: #099;"><span class="idiff">1000</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">progress_update</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>

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192

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<td class="diff-line-num new_line" data-linenumber="192" 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">

192

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="193" 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">

193

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<td class="diff-line-num new_line" data-linenumber="193" 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">

193

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="194" 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">

194

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<td class="diff-line-num new_line" data-linenumber="194" 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">

194

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>

</pre>

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<br>

</li>

<li id="d0edb611a89a0dab9d0dc046d324f550b89d3d03">

<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/20d19355d501e251533c1e6e708100581caffe85#d0edb611a89a0dab9d0dc046d324f550b89d3d03"><strong>src/pytransit/transit_gui.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1757" 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="1757" 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">@@ -1757,7 +1757,7 @@ along with TRANSIT.  If not, see <http://www.gnu.org/licenses/>.</td>

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<td class="diff-line-num old_line" data-linenumber="1757" 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">

1757

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<td class="diff-line-num new_line" data-linenumber="1757" 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">

1757

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<pre style="margin: 0;"> <span id="LC1757" class="line" lang="python">        <span class="n" style="color: #333;">window</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1758" 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">

1758

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<td class="diff-line-num new_line" data-linenumber="1758" 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">

1758

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<pre style="margin: 0;"> <span id="LC1758" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">K</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1759" 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">

1759

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<td class="diff-line-num new_line" data-linenumber="1759" 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">

1759

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<pre style="margin: 0;"> <span id="LC1759" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1760

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<td class="diff-line-num new_line old" data-linenumber="1760" style="width: 35px; color: rgba(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="LC1760" class="line" lang="python">            <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">window</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1761" style="width: 35px; color: rgba(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="1760" style="width: 35px; color: rgba(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="LC1760" class="line" lang="python">            <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">window</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># python3 requires explicit rounding to int</span></span></span>

</pre>

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1761

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<td class="diff-line-num new_line" data-linenumber="1761" 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">

1761

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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="python">            <span class="n" style="color: #333;">x_w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1762" 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">

1762

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<td class="diff-line-num new_line" data-linenumber="1762" 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">

1762

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<pre style="margin: 0;"> <span id="LC1762" class="line" lang="python">            <span class="n" style="color: #333;">y_w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">zeros</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1763" 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">

1763

</td>

<td class="diff-line-num new_line" data-linenumber="1763" 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">

1763

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<pre style="margin: 0;"> <span id="LC1763" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1767" 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="1767" 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">@@ -1767,7 +1767,7 @@ along with TRANSIT.  If not, see <http://www.gnu.org/licenses/>.</td>

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<td class="diff-line-num old_line" data-linenumber="1767" 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">

1767

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<td class="diff-line-num new_line" data-linenumber="1767" 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">

1767

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

<pre style="margin: 0;"> <span id="LC1767" class="line" lang="python">            <span class="n" style="color: #333;">y_smooth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat_tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loess</span><span class="p">(</span><span class="n" style="color: #333;">x_w</span><span class="p">,</span> <span class="n" style="color: #333;">y_w</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10000</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1768" 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">

1768

</td>

<td class="diff-line-num new_line" data-linenumber="1768" 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">

1768

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<pre style="margin: 0;"> <span id="LC1768" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">x_w</span><span class="p">,</span> <span class="n" style="color: #333;">y_w</span><span class="p">,</span> <span class="s" style="color: #d14;">"g+"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1769" 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">

1769

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<td class="diff-line-num new_line" data-linenumber="1769" 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">

1769

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<pre style="margin: 0;"> <span id="LC1769" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">x_w</span><span class="p">,</span> <span class="n" style="color: #333;">y_smooth</span><span class="p">,</span> <span class="s" style="color: #d14;">"b-"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1770

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<pre style="margin: 0;">-<span id="LC1770" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xlabel</span><span class="p">(</span><span class="s" style="color: #d14;">"Genomic Position"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1771" style="width: 35px; color: rgba(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="1770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1770

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<pre style="margin: 0;">+<span id="LC1770" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xlabel</span><span class="p">(</span><span class="s" style="color: #d14;">"Genomic Position<span class="idiff left right"> (TA sites)</span>"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1771" 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">

1771

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<td class="diff-line-num new_line" data-linenumber="1771" 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">

1771

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<pre style="margin: 0;"> <span id="LC1771" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ylabel</span><span class="p">(</span><span class="s" style="color: #d14;">"Reads per 100 insertion sites"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1772" 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">

1772

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<td class="diff-line-num new_line" data-linenumber="1772" 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">

1772

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<pre style="margin: 0;"> <span id="LC1772" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1773" 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">

1773

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<td class="diff-line-num new_line" data-linenumber="1773" 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">

1773

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<pre style="margin: 0;"> <span id="LC1773" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">title</span><span class="p">(</span><span class="s" style="color: #d14;">"LOESS Fit - </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">transit_tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">datasets_selected</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="p">)</span></span>

</pre>

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