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<h3>
Michael R. Crusoe 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/cad37841e08d266124e4f6f971a2e2aad871a44c">cad37841</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-08T17:06:43Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.1</pre>
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<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#95fc4dffde2689028ad133233a529fa3619cb18b">
src/pytpp/__main__.py
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<li class="file-stats">
<a href="#88e0c8b85bd56c1ffb341f3c428ad72e4c8fc7c7">
src/pytpp/tpp_tools.py
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<li class="file-stats">
<a href="#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">
src/pytransit/__init__.py
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<li class="file-stats">
<a href="#ceace322bc3b80ee493350527cac7669ad632158">
src/pytransit/__main__.py
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<li class="file-stats">
<a href="#8f7b871a787b5d5c5b3a11bed95337c59a510906">
src/pytransit/analysis/gi.py
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<a href="#76c26c0b98a2a81031b19761686bcc91a1a9da51">
<span class="deleted-file">
−
src/pytransit/analysis/multitnseq.py
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<a href="#248de6f0e54431894dd74588d32165ead2015eb5">
<span class="deleted-file">
−
src/pytransit/analysis/multitnseq_helpers.py
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<li class="file-stats">
<a href="#8e11d91610ba5cb2818cb8b617ccef1599a952fd">
src/pytransit/analysis/pathway_enrichment.py
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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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 3.0.1 2019-08-01</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p"> -</span> Add check for python3 (TRANSIT 3+ requires python3.6+)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p"> -</span> Minor fixes in GI and Pathway Enrichment</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.0.0 2019-07-18</span></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p"> -</span> TRANSIT now supports python 3. (To use with python 2, use releases < 3.0.0)</span>
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<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">From</span><span class="s" style="color: #d14;"> r-base:3.<span class="idiff left right">4</span>.1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(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="1" style="width: 35px; color: rgba(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="LC2" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="nt" style="color: #000080;">-y</span> <span class="o" style="font-weight: 600;">&&</span> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="nt" style="color: #000080;">-f</span> python<span class="idiff left right">2 python-dev python</span>-pip</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">From</span><span class="s" style="color: #d14;"> r-base:3.<span class="idiff left right">6</span>.1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="nt" style="color: #000080;">-y</span> <span class="o" style="font-weight: 600;">&&</span> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="nt" style="color: #000080;">-f</span> python<span class="idiff left right">3 python-dev python3</span>-pip</span>
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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">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">ADD</span><span class="s" style="color: #d14;"> src/ /src</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="docker"><span class="k" style="font-weight: 600;">ADD</span><span class="s" style="color: #d14;"> tests/ /tests</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip<span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">install </span></span><span class="idiff">pytest </span><span class="s1" style="color: #d14;"><span class="idiff">'numpy~=1.15'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'scipy~=1.2'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'matplotlib~=2.2'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'pillow~=5.0'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'statsmodels~=0.9'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff right">'rpy2<2.9.0</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip<span class="idiff left">3 </span><span class="nb" style="color: #0086b3;"><span class="idiff">install </span></span><span class="idiff">pytest </span><span class="s1" style="color: #d14;"><span class="idiff">'numpy~=1.16'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'scipy~=1.2'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'matplotlib~=3.0'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'pillow~=6.0'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'statsmodels~=0.9'</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff right">'rpy2</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>R <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"install.packages('MASS')"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>R <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"install.packages('pscl')"</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="docker"></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># TRANSIT</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/tag/mad-lab/transit.svg</span><span class="p">)</span>](https://github.com/mad-lab/transit) <span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/mad-lab/transit.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/mad-lab/transit) <span class="p">[</span><span class="nv" style="color: #008080;">![Documentation Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/projects/transit/badge/?version=latest</span><span class="p">)</span>](http://transit.readthedocs.io/en/latest/?badge=latest) <span class="p">[</span><span class="nv" style="color: #008080;">![Downloads</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pepy.tech/badge/tnseq-transit</span><span class="p">)</span>](https://pepy.tech/project/tnseq-transit)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">=======</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**NOTE: TRANSIT v3.0+ now requires python3.6+. If you want to use TRANSIT with python2, use version < 3.0.**</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown">Welcome! This is the distribution for the TRANSIT and TPP tools developed by the <span class="p">[</span><span class="nv" style="color: #008080;">Ioerger Lab</span><span class="p">](</span><span class="sx" style="color: #d14;">http://orca2.tamu.edu/tom/iLab.html</span><span class="p">)</span> at Texas A&M University.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">TRANSIT is a tool for processing and statistical analysis of Tn-Seq data.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +25,7 @@ TRANSIT offers a variety of features including:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="p">-</span> Ability to analyze datasets from libraries constructed using <span class="gs" style="font-weight: 600;">**himar1 or tn5 transposons**</span>.</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="p">-</span> <span class="gs" style="font-weight: 600;">**TrackView**</span> to help visualize read-counts ac<span class="idiff left right">c</span>ross the genome.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p">-</span> <span class="gs" style="font-weight: 600;">**TrackView**</span> to help visualize read-counts across the genome.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="p">-</span> Can <span class="gs" style="font-weight: 600;">**export datasets**</span> into a variety of formats, including <span class="gs" style="font-weight: 600;">**IGV**</span>.</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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">@@ -101,6 +101,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text/markdown'</span><span class="p">,</span></span>
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104
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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105
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The project's main homepage.</span></span>
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106
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/mad-lab/transit'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#95fc4dffde2689028ad133233a529fa3619cb18b"><strong>src/pytpp/__main__.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">@@ -39,6 +39,10 @@ def run_main():</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check python version</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"TRANSIT v3.0+ requires python3.6+. To use with python2, please install TRANSIT version < 3.0"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" 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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42
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="nb" style="color: #0086b3;">vars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Globals</span><span class="p">()</span></span>
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43
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check for arguements</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">kwargs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">hasWx</span><span class="p">:</span> </span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#88e0c8b85bd56c1ffb341f3c428ad72e4c8fc7c7"><strong>src/pytpp/tpp_tools.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">@@ -1442,6 +1442,7 @@ def show_help():</td>
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1442
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' -maxreads <INT>'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' -mismatches <INT> # when searching for constant regions in reads 1 and 2; default is 1'</span><span class="p">)</span></span>
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1444
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' -flags "<STRING>" # args to pass to BWA'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' -bwa-alg [aln|mem] # Default: mem. Algorithm to use for mapping reads with bwa'</span> <span class="p">)</span></span>
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1445
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1446
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' -primer-start-window INT,INT # position in read to search for start of primer; default is [0,20]'</span><span class="p">)</span></span>
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1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' -window-size INT # automatic method to set window'</span><span class="p">)</span></span>
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1448
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' -barseq_catalog_in|-barseq_catalog_out <file>'</span><span class="p">)</span></span>
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<li id="176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">
<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4"><strong>src/pytransit/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,6 @@</td>
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2
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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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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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5
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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">0</span>"</span></span>
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5
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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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6
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6
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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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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#ceace322bc3b80ee493350527cac7669ad632158"><strong>src/pytransit/__main__.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">@@ -43,6 +43,10 @@ def run_main():</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check python version</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"TRANSIT v3.0+ requires python3.6+. To use with python2, please install TRANSIT version < 3.0"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" 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="LC50" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#If no arguments, show GUI:</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">DEBUG</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--debug"</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>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">DEBUG</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#8f7b871a787b5d5c5b3a11bed95337c59a510906"><strong>src/pytransit/analysis/gi.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">@@ -40,10 +40,10 @@ long_name = "Genetic Interactions"</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="n" style="color: #333;">short_desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Genetic interactions analysis for change in enrichment"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">long_desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""Method for determining genetic interactions based on changes in enrichment (i.e. delta log fold-change in mean read counts).</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;">NOTE: This method requires 4 groups of datasets. Use the main interface to add datasets for the two strain backgrounds under the first condition. A window will allow you to add the datasets under the second condition.</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;">NOTE: This method requires 4 groups of datasets. Use the main interface to add datasets for the two strain backgrounds under the first condition. A<span class="idiff left right">fter pressing "Run GI", a subsequent</span> window will allow you to add the datasets under the second condition.</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">transposons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">transposons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left right">"himar1"</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Orf"</span><span class="p">,</span><span class="s" style="color: #d14;">"Name"</span><span class="p">,</span><span class="s" style="color: #d14;">"Number of TA Sites"</span><span class="p">,</span><span class="s" style="color: #d14;">"Mean count (Strain A Condition 1)"</span><span class="p">,</span><span class="s" style="color: #d14;">"Mean count (Strain A Condition 2)"</span><span class="p">,</span><span class="s" style="color: #d14;">"Mean count (Strain B Condition 1)"</span><span class="p">,</span><span class="s" style="color: #d14;">"Mean count (Strain B Condition 2)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Mean logFC (Strain A)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Mean logFC (Strain B)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Mean delta logFC"</span><span class="p">,</span><span class="s" style="color: #d14;">"Lower Bound delta logFC"</span><span class="p">,</span><span class="s" style="color: #d14;">"Upper Bound delta logFC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Prob. of delta-logFC being within ROPE"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Adjusted Probability (BFDR)"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Is HDI outside ROPE?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Type of Interaction"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#76c26c0b98a2a81031b19761686bcc91a1a9da51"><strong>src/pytransit/analysis/multitnseq.py</strong>
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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>
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<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;">os</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">io</span></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;">hasR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">rpy2.robjects</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">hasR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">hasR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">base</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pdfkit</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">statsmodels.stats.multitest</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">statsmodels.stats.multicomp</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytransit.transit_tools</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">transit_tools</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytransit.tnseq_tools</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tnseq_tools</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytransit.norm_tools</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">norm_tools</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multitnseq_helpers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">def_r_samples_corrplot</span><span class="p">,</span> <span class="n" style="color: #333;">def_r_clustering</span><span class="p">,</span> <span class="n" style="color: #333;">def_r_make_heatmap</span><span class="p">,</span> <span class="n" style="color: #333;">def_r_conditions_corrplot</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">###### GUI ELEMENTS ######</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">short_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"MultiTnSeq"</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">long_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"MultiTnSeq"</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="n" style="color: #333;">short_desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Run the MultiTnSeq pipeline"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">long_desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""Run the MultiTnSeq pipeline"""</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">transposons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">EOL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MultiTnSeqAnalysis</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TransitAnalysis</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TransitAnalysis</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">short_name</span><span class="p">,</span> <span class="n" style="color: #333;">long_name</span><span class="p">,</span> <span class="n" style="color: #333;">short_desc</span><span class="p">,</span> <span class="n" style="color: #333;">long_desc</span><span class="p">,</span> <span class="n" style="color: #333;">transposons</span><span class="p">,</span> <span class="n" style="color: #333;">MultiTnSeqMethod</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MultiTnSeqMethod</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">AnalysisMethod</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> MultiTnSeq pipeline, uses R scripts</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fna</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">cond_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">K</span><span class="p">,</span> <span class="n" style="color: #333;">D</span><span class="p">,</span> <span class="n" style="color: #333;">debatch</span><span class="p">,</span> <span class="n" style="color: #333;">stdnorm</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">AnalysisMethod</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">short_name</span><span class="p">,</span> <span class="n" style="color: #333;">long_name</span><span class="p">,</span> <span class="n" style="color: #333;">short_desc</span><span class="p">,</span> <span class="n" style="color: #333;">long_desc</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" 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;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fna</span></span>
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<pre style="margin: 0;">-<span id="LC42" 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;">annotation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotation</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">combined_wig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combined_wig</span></span>
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<pre style="margin: 0;">-<span id="LC44" 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;">samples_metadata_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span></span>
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<pre style="margin: 0;">-<span id="LC45" 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;">conditions_metadata_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cond_metadata</span></span>
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<pre style="margin: 0;">-<span id="LC46" 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_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_file</span></span>
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<pre style="margin: 0;">-<span id="LC47" 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;">K</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">K</span></span>
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<pre style="margin: 0;">-<span id="LC48" 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;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">D</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" 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;">debatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" 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;">stdnorm</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" 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;">rundir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fromargs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">rawargs</span><span class="p">):</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">hasR</span><span class="p">:</span></span>
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56
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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 class="p">(</span><span class="s" style="color: #d14;">"Error: R and rpy2 (< 2.9.0) required to run ZINB analysis."</span><span class="p">)</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"After installing R, you can install rpy2 using the command </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">pip install 'rpy2<2.9.0'</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" 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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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"></span>
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60
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<pre style="margin: 0;">-<span id="LC60" 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>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'-help'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'h'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)):</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">MultiTnSeqMethod</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">usage_string</span><span class="p">())</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" 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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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">fna</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>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">annotation</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>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">combined_wig</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>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">metadata</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>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">cond_metadata</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>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">output_file</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>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">K</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"K"</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"D"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">debatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-debatch"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">stdnorm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-stdnorm"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">(</span><span class="n" style="color: #333;">fna</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">cond_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">K</span><span class="p">,</span> <span class="n" style="color: #333;">D</span><span class="p">,</span> <span class="n" style="color: #333;">debatch</span><span class="p">,</span> <span class="n" style="color: #333;">stdnorm</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_genes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC81" 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>
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<pre style="margin: 0;">-<span id="LC82" 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;">split</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="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span 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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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;">2</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="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">descriptions</span><span class="o" style="font-weight: 600;">==</span><span class="bp" style="color: #999;">True</span><span class="p">:</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">w</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="LC85" 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;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">genes</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_genome</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <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>
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91
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<pre style="margin: 0;">-<span id="LC91" 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;">filename</span><span class="p">):</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" 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="n" style="color: #333;">n</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;"># skip first</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">line</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hash_genes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">genome</span><span class="p">):</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="nb" style="color: #0086b3;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" 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>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" 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;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="nb" style="color: #0086b3;">hash</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="n" style="color: #333;">gene</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">hash</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">makefname</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span><span class="nb" style="color: #0086b3;">dir</span><span class="p">):</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">""</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span></span>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</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="nb" style="color: #0086b3;">dir</span><span class="p">,</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">Run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Running"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.generate_pdf()</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.transit_message("Done.")</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC113" 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;">tnseq_tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Spreadsheet</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;">makefname</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;">samples_metadata_fname</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;">rundir</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">Conditions</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;">Spreadsheet</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;">makefname</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;">conditions_metadata_fname</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;">rundir</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">genome</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;">read_genome</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;">makefname</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;">ref</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;">rundir</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">genes</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;">read_genes</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;">makefname</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;">annotation</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;">rundir</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">ghash</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;">hash_genes</span><span class="p">(</span><span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">genome</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">datasets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcol</span><span class="p">(</span><span class="s" style="color: #d14;">"Filename"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># filenames</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">filenamesInCombWig</span><span class="p">)</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_combined_wig</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;">makefname</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;">combined_wig</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;">rundir</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># data: rows are TA sites, cols are datasets</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "datasets" are columns (indexes) in combined wig (data)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># SampleIndexes are list of rows in Samples to be analyzed (contains Filenames and Conditions), i.e. which datasets (row indexes in data) represent each condition?</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># wigindexes are corresponding columns in data (from original order, matched by Filename)</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">SampleIndexes</span><span class="p">,</span><span class="n" style="color: #333;">wigindexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[]</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cond</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</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;">Samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Samples</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;">row</span><span class="p">,</span><span class="s" style="color: #d14;">"Condition"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cond</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Samples</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;">row</span><span class="p">,</span><span class="s" style="color: #d14;">"Filename"</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filenamesInCombWig</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"error: filename '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' listed in samples metadata not found in combined wig file"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fname</span><span class="p">;</span> <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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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">SampleIndexes</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;">row</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">wigindexes</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;">filenamesInCombWig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">))</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># reordering data matrix (select columns, order by cond) for normalization; now should be parallel to SampleIndexes</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">wigindexes</span><span class="p">,</span> <span class="p">:]</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">wigindexes</span><span class="p">,</span> <span class="p">:]</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">neworder</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">filenamesInCombWig</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wigindexes</span><span class="p">]</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">filenamesInData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">neworder</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># foreach cond, list of indexes into data</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">cond2datasets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cond</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">:</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">cond2datasets</span><span class="p">[</span><span class="n" style="color: #333;">cond</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</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;">Samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Samples</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;">row</span><span class="p">,</span><span class="s" style="color: #d14;">"Condition"</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">cond</span><span class="p">:</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Samples</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;">row</span><span class="p">,</span><span class="s" style="color: #d14;">"Filename"</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">cond2datasets</span><span class="p">[</span><span class="n" style="color: #333;">cond</span><span class="p">]</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;">filenamesInData</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">))</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" 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;">cond2datasets</span><span class="p">[</span><span class="n" style="color: #333;">cond</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"error: no samples found in metadata for condition </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;">cond</span><span class="p">;</span> <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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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">normed</span><span class="p">,</span> <span class="n" style="color: #333;">factors</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">norm_tools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normalize_data</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'TTR'</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">Nds</span><span class="p">,</span><span class="n" style="color: #333;">Nsites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normed</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="c1" style="color: #998; font-style: italic;"># transposed: rows are datasets, cols are TA sites</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" 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;">makefname</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_counts_TTR.txt"</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;">rundir</span><span class="p">),</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"coord ORF gene"</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="n" style="color: #333;">Samples</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;">r</span><span class="p">,</span><span class="s" style="color: #d14;">"Id"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SampleIndexes</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># in order of Conditions</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" 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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160
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<pre style="margin: 0;">-<span id="LC160" 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;">sites</span><span class="p">):</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">rv</span><span class="p">,</span><span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"igr"</span><span class="p">,</span><span class="s" style="color: #d14;">"igr"</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">co</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ghash</span><span class="p">:</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">annot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ghash</span><span class="p">[</span><span class="n" style="color: #333;">co</span><span class="p">]</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">rv</span><span class="p">,</span><span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annot</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">annot</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" 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;">str</span><span class="p">(</span><span class="n" style="color: #333;">co</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="o" style="font-weight: 600;">+</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="p">(</span><span class="nb" style="color: #0086b3;">int</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="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">normed</span><span class="p">[:,</span><span class="n" style="color: #333;">i</span><span class="p">])]</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" 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="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 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="LC167" 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;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">r_correlation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">def_r_samples_corrplot</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">r_correlation</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_counts_TTR.txt"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># write table of stats (saturation,NZmean)</span></span>
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<pre style="margin: 0;">-<span id="LC173" 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;">makefname</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_stats.txt"</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;">rundir</span><span class="p">),</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" 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;">"dataset</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">density</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">mean_ct</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NZmean</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NZmedian</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">max_ct</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">total_cts</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">skewness</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kurtosis</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC175" 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;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">density</span><span class="p">,</span> <span class="n" style="color: #333;">meanrd</span><span class="p">,</span> <span class="n" style="color: #333;">nzmeanrd</span><span class="p">,</span> <span class="n" style="color: #333;">nzmedianrd</span><span class="p">,</span> <span class="n" style="color: #333;">maxrd</span><span class="p">,</span> <span class="n" style="color: #333;">totalrd</span><span class="p">,</span> <span class="n" style="color: #333;">skew</span><span class="p">,</span> <span class="n" style="color: #333;">kurtosis</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;">get_data_stats</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,:])</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" 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;">filenamesInData</span><span class="p">[</span><span class="n" style="color: #333;">i</span><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;">density</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;">meanrd</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;">nzmeanrd</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="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">nzmedianrd</span><span class="p">,</span> <span class="n" style="color: #333;">maxrd</span><span class="p">,</span> <span class="n" style="color: #333;">totalrd</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;">skew</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;">kurtosis</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC178" 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="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 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="LC179" 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;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">################################</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># new version, hashes on Rv</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">siteshash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" 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;">TA</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;">sites</span><span class="p">):</span> <span class="n" style="color: #333;">siteshash</span><span class="p">[</span><span class="n" style="color: #333;">TA</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">TAsites</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g</span><span class="p">,(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</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;">genes</span><span class="p">):</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">siteindexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" 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;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># end+1?</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">co</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="mi" style="color: #099;">1</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">co</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">siteshash</span><span class="p">:</span> <span class="n" style="color: #333;">siteindexes</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;">siteshash</span><span class="p">[</span><span class="n" style="color: #333;">co</span><span class="p">])</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">TAsites</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="n" style="color: #333;">siteindexes</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># print means for each gene for each dataset</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" 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="n" style="color: #333;">filenamesInData</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" 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="n" style="color: #333;">Samples</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;">x</span><span class="p">,</span><span class="s" style="color: #d14;">"Id"</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;">SampleIndexes</span><span class="p">])</span></span>
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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" 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;">TAsites</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;">0</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># skip genes with no TA sites</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" 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>
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<pre style="margin: 0;">-<span id="LC204" 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;">Nds</span><span class="p">):</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normed</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">TAsites</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]]</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">means</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;">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;">obs</span><span class="p">))</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" 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="n" style="color: #333;">Rv</span><span class="p">,</span><span class="n" style="color: #333;">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;">TAsites</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="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;">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;">means</span><span class="p">])</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#sys.exit(0)</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC211" 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 class="c1" style="color: #998; font-style: italic;"># sub-arrays of (datasets X sites) for genes X conds, where #TAs>0</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">siteindexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TAsites</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">local</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normed</span><span class="p">[:,</span><span class="n" style="color: #333;">siteindexes</span><span class="p">]</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" 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>
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216
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<pre style="margin: 0;">-<span id="LC216" 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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">cond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Conditions</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;">j</span><span class="p">,</span><span class="s" style="color: #d14;">"Condition"</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">local</span><span class="p">[</span><span class="n" style="color: #333;">cond2datasets</span><span class="p">[</span><span class="n" style="color: #333;">cond</span><span class="p">],:]</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" 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;">obs</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># sub-matrices</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">Counts</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="n" style="color: #333;">counts</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"></span>
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222
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<pre style="margin: 0;">-<span id="LC222" 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>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC224" 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;">TAsites</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;">0</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># skip genes with no TA sites</span></span>
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<pre style="margin: 0;">-<span id="LC225" 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>
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<pre style="margin: 0;">-<span id="LC226" 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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">cond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Conditions</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;">j</span><span class="p">,</span><span class="s" style="color: #d14;">"Condition"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counts</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">means</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;">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;">obs</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">Means</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="n" style="color: #333;">means</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC232" 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;">makefname</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_gene_means.txt"</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;">rundir</span><span class="p">),</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC233" 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="s" style="color: #d14;">"ORF 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 class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcol</span><span class="p">(</span><span class="s" style="color: #d14;">'Condition'</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="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Means</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># skip genes with no TA sites</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">means</span><span class="p">,</span><span class="n" style="color: #333;">sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">],</span><span class="n" style="color: #333;">TAsites</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC237" 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;">Rv</span><span class="p">,</span><span class="n" style="color: #333;">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;">sites</span><span class="p">))]</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;">%0.1</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;">means</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="LC238" 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;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">################################</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># do ANOVA to identify genes with significant variability</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># it is much faster to do this in python than R (and don't have to create the melted file)</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span><span class="p">,</span><span class="n" style="color: #333;">Rvs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[]</span> <span class="c1" style="color: #998; font-style: italic;"># lists</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Means</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">countsvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counts</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">countsvec</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="n" style="color: #333;">flatten</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;">countsvec</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">stat</span><span class="p">,</span><span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scipy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">f_oneway</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">countsvec</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC250" 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="n" style="color: #333;">pval</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">Rvs</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;">Rv</span><span class="p">)</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="n" style="color: #333;">pvals</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;">pvals</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">mask</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;">isfinite</span><span class="p">(</span><span class="n" style="color: #333;">pvals</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">qvals</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;">full</span><span class="p">(</span><span class="n" style="color: #333;">pvals</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</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;">nan</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">qvals</span><span class="p">[</span><span class="n" style="color: #333;">mask</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">statsmodels</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">multitest</span><span class="o" style="font-weight: 600;">.</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="n" style="color: #333;">mask</span><span class="p">])[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># BH, alpha=0.05</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">,</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},{}</span></span>
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<pre style="margin: 0;">-<span id="LC259" 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;">rv</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;">Rvs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">rv</span><span class="p">],</span><span class="n" style="color: #333;">q</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="n" style="color: #333;">pvals</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="n" style="color: #333;">qvals</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="LC261" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span><span class="p">,</span><span class="n" style="color: #333;">qvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">,</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># hashes on Rv</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># post-hoc analysis to identify "high" and "low" subgroups</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">Sortedmeans</span><span class="p">,</span><span class="n" style="color: #333;">Divisions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},{}</span> <span class="c1" style="color: #998; font-style: italic;"># sortedmeans: list of (mean,cond); divisions: list of (lowsubset,highsubset) or None</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">qvals</span> <span class="ow" style="font-weight: 600;">and</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="mf" style="color: #099;">0.05</span><span class="p">:</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print Rv,gene</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">countsvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counts</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">countsvec</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="n" style="color: #333;">flatten</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;">countsvec</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">allcounts</span><span class="p">,</span><span class="n" style="color: #333;">allconds</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;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([])</span></span>
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<pre style="margin: 0;">-<span id="LC271" 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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">)):</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">allcounts</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;">append</span><span class="p">(</span><span class="n" style="color: #333;">allcounts</span><span class="p">,</span><span class="n" style="color: #333;">countsvec</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">countsvec</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])):</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">allconds</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;">append</span><span class="p">(</span><span class="n" style="color: #333;">allconds</span><span class="p">,</span><span class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">mc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">statsmodels</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">multicomp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MultiComparison</span><span class="p">(</span><span class="n" style="color: #333;">allcounts</span><span class="p">,</span><span class="n" style="color: #333;">allconds</span><span class="p">)</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">tuk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tukeyhsd</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># alpha=0.1</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print tuk</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">reject</span><span class="p">,</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},</span><span class="mi" style="color: #099;">0</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tuk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groupsunique</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">group1</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;">groups</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC281" 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;">group2</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;">groups</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC282" 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;">k</span><span class="p">:</span> <span class="n" style="color: #333;">reject</span><span class="p">[(</span><span class="n" style="color: #333;">group1</span><span class="p">,</span><span class="n" style="color: #333;">group2</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reject</span><span class="p">[(</span><span class="n" style="color: #333;">group2</span><span class="p">,</span><span class="n" style="color: #333;">group1</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tuk</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reject</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="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">sortedmeans</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;">mean</span><span class="p">(</span><span class="n" style="color: #333;">countsvec</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]),</span><span class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">countsvec</span><span class="p">))]</span> <span class="c1" style="color: #998; font-style: italic;"># list of (mean,condname)</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">sortedmeans</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">sortedmeans</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">Sortedmeans</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="n" style="color: #333;">sortedmeans</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">sortedgroups</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="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;">sortedmeans</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#for (m,c) in sortedmeans: print c,"%0.1f" % m</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">candidate_divisions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># lists of condition names in 2 subgroups (lower and higher, but not necessarily in that order)</span></span>
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<pre style="margin: 0;">-<span id="LC289" 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="mi" style="color: #099;">1</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sortedmeans</span><span class="p">)):</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">lowsubset</span><span class="p">,</span><span class="n" style="color: #333;">highsubset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortedgroups</span><span class="p">[:</span><span class="n" style="color: #333;">j</span><span class="p">],</span><span class="n" style="color: #333;">sortedgroups</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">:]</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">alldistinct</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lowsubset</span><span class="p">:</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">highsubset</span><span class="p">:</span> <span class="n" style="color: #333;">alldistinct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alldistinct</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">reject</span><span class="p">[(</span><span class="n" style="color: #333;">group1</span><span class="p">,</span><span class="n" style="color: #333;">group2</span><span class="p">)];</span> <span class="c1" style="color: #998; font-style: italic;"># print group1,group2,reject[(group1,group2)]</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortedmeans</span><span class="p">[</span><span class="n" style="color: #333;">j</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;">sortedmeans</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 class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># could be negative if conds not sorted</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lowsubset</span><span class="o" style="font-weight: 600;">+</span><span class="p">[</span><span class="s" style="color: #d14;">'<<<--->>>'</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highsubset</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;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">alldistinct</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;">diff</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print '\t'.join(vals)</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">diff</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;">diff</span><span class="p">,</span><span class="n" style="color: #333;">lowsubset</span><span class="p">,</span><span class="n" style="color: #333;">highsubset</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">diff</span><span class="p">,</span><span class="n" style="color: #333;">highsubset</span><span class="p">,</span><span class="n" style="color: #333;">lowsubset</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alldistinct</span><span class="o" style="font-weight: 600;">==</span><span class="bp" style="color: #999;">True</span><span class="p">:</span> <span class="n" style="color: #333;">candidate_divisions</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;">diff</span><span class="p">,</span><span class="n" style="color: #333;">lowsubset</span><span class="p">,</span><span class="n" style="color: #333;">highsubset</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC299" 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;">candidate_divisions</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">candidate_divisions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">diff</span><span class="p">,</span><span class="n" style="color: #333;">lowsubset</span><span class="p">,</span><span class="n" style="color: #333;">highsubset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">candidate_divisions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">Divisions</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;">lowsubset</span><span class="p">,</span><span class="n" style="color: #333;">highsubset</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#The tukeyhsd of statsmodels doesn't return P value.</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#So, if you want to know P value, calculate from these outputted value or use R.</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#After saving the output into a variable res, you can get p-values by applying</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># psturng(np.abs(res.meandiffs / res.std_pairs), len(res.groupsunique), res.df_total), where psturng comes from from statsmodels.stats.libqsturng import psturng</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># save pvals as temp_anova.txt</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" 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;">makefname</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_anova.txt"</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;">rundir</span><span class="p">),</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</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 class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;">+</span><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>
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312
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<pre style="margin: 0;">-<span id="LC312" 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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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Means</span><span class="p">:</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="p">,</span><span class="n" style="color: #333;">s</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 class="n" style="color: #333;">Rv</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;">std</span><span class="p">(</span><span class="n" style="color: #333;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">])</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">scv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">m</span></span>
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<pre style="margin: 0;">-<span id="LC317" 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="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;">TAsites</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="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;">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;">Means</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="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="c1" style="color: #998; font-style: italic;"># could append SCV, but beware of how multi_TnSeq.py counts hits in temp_anova.txt</span></span>
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<pre style="margin: 0;">-<span id="LC318" 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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<pre style="margin: 0;">-<span id="LC319" 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;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># write sorted means and high/low subgroups into temp_subgroups.txt</span></span>
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<pre style="margin: 0;">-<span id="LC322" 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;">makefname</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_divisions.txt"</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;">rundir</span><span class="p">),</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</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 class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span></span>
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<pre style="margin: 0;">-<span id="LC324" 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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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">qvals</span> <span class="ow" style="font-weight: 600;">and</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="mf" style="color: #099;">0.05</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC327" 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="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;">TAsites</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="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;">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;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]]</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" 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;">x</span><span class="p">[</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;">Sortedmeans</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="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;">x</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;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Sortedmeans</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Divisions</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">lowsubset</span><span class="p">,</span><span class="n" style="color: #333;">highsubset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Divisions</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC331" 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="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;">lowsubset</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="n" style="color: #333;">highsubset</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC332" 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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<pre style="margin: 0;">-<span id="LC333" 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;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># print gene means for each condition, and batch means</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC338" 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>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Means</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">batches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Conditions</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;">r</span><span class="p">,</span><span class="s" style="color: #d14;">"Batch"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">batch</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">batches</span><span class="p">:</span> <span class="n" style="color: #333;">batches</span><span class="p">[</span><span class="n" style="color: #333;">batch</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">batches</span><span class="p">[</span><span class="n" style="color: #333;">batch</span><span class="p">]</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;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">r</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">vals</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;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">r</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;">###</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"CC1 CC2 CC3 KO"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">():</span> <span class="n" style="color: #333;">vals</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;">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;">batches</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC347" 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="n" style="color: #333;">Rv</span><span class="p">,</span><span class="n" style="color: #333;">gene</span><span class="p">]</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;">%0.1</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;">vals</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;">###</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">###sys.exit(0)</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># remove batch effects (subtract batch means from mean gene counts; adjust each to global mean)</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debatch</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"Batch"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">headers</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"<BR>correcting means for batch effects..."</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Means</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">batches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Conditions</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;">r</span><span class="p">,</span><span class="s" style="color: #d14;">"Batch"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">batch</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">batches</span><span class="p">:</span> <span class="n" style="color: #333;">batches</span><span class="p">[</span><span class="n" style="color: #333;">batch</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">batches</span><span class="p">[</span><span class="n" style="color: #333;">batch</span><span class="p">]</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;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">r</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">globalmean</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 class="n" style="color: #333;">Rv</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">batches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">batchmeans</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">:</span> <span class="n" style="color: #333;">batchmeans</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">]</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;">batches</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Conditions</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;">r</span><span class="p">,</span><span class="s" style="color: #d14;">"Batch"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">delta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">globalmean</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">batchmeans</span><span class="p">[</span><span class="n" style="color: #333;">batch</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># correction for each batch</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">r</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">delta</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># print gene means for each condition (with batch corrections)</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" 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="s" style="color: #d14;">'ORF'</span><span class="p">,</span><span class="s" style="color: #d14;">'gene'</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcol</span><span class="p">(</span><span class="s" style="color: #d14;">"Condition"</span><span class="p">)</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" 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="n" style="color: #333;">vals</span><span class="p">)</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Means</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" 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;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">)]</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" 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="n" style="color: #333;">Rv</span><span class="p">,</span><span class="n" style="color: #333;">gene</span><span class="p">]</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;">%0.1</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;">vals</span><span class="p">])</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" 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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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">################################</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># calc LFCs</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># consider normalizing by reference conditions?</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># consider only calculating for non-reference conditions?</span></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"></span>
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388
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<pre style="margin: 0;">-<span id="LC388" 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>
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<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">qvals</span> <span class="ow" style="font-weight: 600;">and</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="mf" style="color: #099;">0.05</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">lfcvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC392" 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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># could remove means for reference conditions</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">b</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;">median</span><span class="p">(</span><span class="n" style="color: #333;">Means</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC395" 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>
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<pre style="margin: 0;">-<span id="LC396" 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;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">5</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;">b</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">5</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">lfcvec</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;">lfc</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">lfcs</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="n" style="color: #333;">lfcvec</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdnorm</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"<BR>applying standard normalization to LFCs"</span></span>
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<pre style="margin: 0;">-<span id="LC402" 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;">cond</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;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">):</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lfcs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()]</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="p">,</span><span class="n" style="color: #333;">s</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;">col</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;">std</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># consider using quantiles(col,[0,0.25,0.5,0.75,1.0])</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lfcs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">lfcs</span><span class="p">[</span><span class="n" style="color: #333;">Rv</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="p">(</span><span class="n" style="color: #333;">lfcs</span><span class="p">[</span><span class="n" style="color: #333;">Rv</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="n" style="color: #333;">m</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">s</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC408" 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;">makefname</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_LFCs.txt"</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;">rundir</span><span class="p">),</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Rv Gene"</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="n" style="color: #333;">Conditions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span> <span class="c1" style="color: #998; font-style: italic;"># or non-ref-conds</span></span>
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<pre style="margin: 0;">-<span id="LC410" 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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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</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="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">qvals</span> <span class="ow" style="font-weight: 600;">and</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="mf" style="color: #099;">0.05</span><span class="p">:</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" 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="o" style="font-weight: 600;">+</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;">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="n" style="color: #333;">Rv</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC415" 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="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 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="LC416" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" 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;">close</span><span class="p">()</span></span>
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418
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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="n" style="color: #333;">cnt</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;">print</span> <span class="s" style="color: #d14;">"error: no significantly varying genes found by ANOVA"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">return</span></span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"></span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">r_conditions_corrplot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">def_r_conditions_corrplot</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">r_make_heatmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">def_r_make_heatmap</span><span class="p">()</span></span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">r_clustering</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">def_r_clustering</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">r_conditions_corrplot</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_LFCs.txt"</span><span class="p">)</span></span>
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425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">r_make_heatmap</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_LFCs.txt"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">r_clustering</span><span class="p">(</span><span class="s" style="color: #d14;">"temp_LFCs.txt"</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;">K</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;">D</span><span class="p">)</span></span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC428" 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;">generate_pdf</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC429" 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;">"Done."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_html</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">stats_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<table border="1" cellpadding="5" cellspacing="0">'</span></span>
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<pre style="margin: 0;">-<span id="LC433" 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="s" style="color: #d14;">"temp_stats.txt"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC434" 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 class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">stats_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"<tr>"</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">w</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">stats_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"<td>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</td>"</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">stats_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"</tr>"</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">stats_table</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'</table>'</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="n" style="color: #333;">lfcs_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/lfcs_boxplot.png"</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">corr_plot</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<p><br>lfcs_boxplot.png:<br><img src="{0}"></p>'</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;">lfcs_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">anova_varying</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">skip</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC446" 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="s" style="color: #d14;">"temp_anova.txt"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># skip header lines</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">skip</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;">skip</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;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC449" 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 class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'nan'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.05</span><span class="p">:</span> <span class="n" style="color: #333;">anova_varying</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">anova_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<p>ANOVA finds {0} significantly varying genes'</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;">anova_varying</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">conditions_corrplot_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/conditions_corrplot.png"</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">conditions_corrplot</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<p><br>conditions_corrplot.png:<br><img src="{0}"></p>'</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;">conditions_corrplot_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">lfcs_heatmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<p><br>heatmap.png:<BR><img src='{0}'></p>"</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/heatmap.png"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">cluster_analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''' '''</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'''</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"><span class="s" style="color: #d14;"> <p></span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"><span class="s" style="color: #d14;"> Links</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="python"><span class="s" style="color: #d14;"> <ul></span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="python"><span class="s" style="color: #d14;"> <li> <a href="temp_stats.txt">spreadsheet of statistics on TnSeq datasets</a></span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"><span class="s" style="color: #d14;"> <li> <a href="temp_counts_TTR.txt">spreadsheet of normalized counts</a></span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"><span class="s" style="color: #d14;"> <li> <a href="temp_anova.txt">spreadsheet with gene means and Anova results</a></span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"><span class="s" style="color: #d14;"> <li> <a href="temp_clust.txt">spreadsheet with LFCs and clusters</a></span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python"><span class="s" style="color: #d14;"> <li> <a href="temp_divisions.txt">spreadsheet with divisions of conditions into low and high subgroups for significantly varying genes </a></span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"><span class="s" style="color: #d14;"> <li> <a href="temp_scores.txt"> spreadsheet with loadings of genes onto Varimax dimensions, along with normalized associations</a></span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"><span class="s" style="color: #d14;"> <li> <a href="PFilteredValues.txt"> text file with enriched functional categories in each clusters</a></span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"><span class="s" style="color: #d14;"> </ul></span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"><span class="s" style="color: #d14;"> </p></span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python"><span class="s" style="color: #d14;"> <H3>Quality Control</H3></span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"><span class="s" style="color: #d14;"> <P>Statistics of TnSeq datasets:<BR></span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"><span class="s" style="color: #d14;"> {stats_table}</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"><span class="s" style="color: #d14;"> {corr_plot}</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"><span class="s" style="color: #d14;"> <hr></span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"><span class="s" style="color: #d14;"> {anova_results}</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"><span class="s" style="color: #d14;"> <br></span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python"><span class="s" style="color: #d14;"> Conditions corrplot is based on significantly varying genes</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="python"><span class="s" style="color: #d14;"> {conditions_corrplot}</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="python"><span class="s" style="color: #d14;"> <hr></span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="python"><span class="s" style="color: #d14;"> <h3>Cluster Analysis</h3></span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"><span class="s" style="color: #d14;"> <p>LFCs are relative to the median across all conditions</p></span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="python"><span class="s" style="color: #d14;"> {lfcs_heatmap}</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">stats_table</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stats_table</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">corr_plot</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">corr_plot</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">anova_results</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">anova_results</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">conditions_corrplot</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">conditions_corrplot</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"> <span class="n" style="color: #333;">lfcs_heatmap</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lfcs_heatmap</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<HR>"</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<H3>Cluster Analysis</H3>"</span></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>LFCs are relative to the median across all conditions"</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/heatmap.png" % dir</span></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<BR>heatmap.png:<BR><img src='%s'>" % newfname</span></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/cluster_opt.png" % dir</span></span>
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500
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC500" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>cluster_opt.png:<BR><img src='%s'>" % newfname</span></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/pca_genes.png" % dir</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>LD-PCA, colored by Kmeans cluster (K=%s)" % K</span></span>
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504
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC504" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<BR>pca_genes.png:<BR><img src='%s'>" % newfname</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/hclust_genes.png" % dir</span></span>
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<td class="diff-line-num old old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>hclust_genes.png:<BR><img src='%s'>" % newfname</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/hclust_conditions.png" % dir</span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>hclust_conditions.png:<BR><img src='%s'>" % newfname</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<HR>"</span></span>
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514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"></span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<H3>Pathway Enrichment</H3>"</span></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"></span>
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517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print """This analysis shows which functional categories are enriched in each cluster.</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># It uses the Sanger annotation (based on Cole's original descriptions of ORF functions,</span></span>
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519
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC519" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># with updates. Only the categories with <I>adjusted p-values</I> < 0.05 are shown below.</span></span>
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520
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC520" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># P-values were calculated using the Hypergeometric distribution, and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># the multiple-test correction by the Benjamini-Hochberg procedure</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># was applied to control the FDR at 5%."""</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># from functionPathWay import sangerClassification</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># sangerRoles="H37Rv.sanger_roles2"</span></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># protTable="%s/ref.prot_table" % dir</span></span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># clusters="%s/temp_clust.txt" %dir</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># resultFileName="%s/PFilteredValues.txt" % dir</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># sangerClassification(sangerRoles,protTable,clusters,resultFileName)</span></span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"></span>
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531
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<PRE>"</span></span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for line in open(resultFileName):</span></span>
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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print line,</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "</PRE>"</span></span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<HR>"</span></span>
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537
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"></span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<H3>Principle Component Analysis</H3>"</span></span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"></span>
</pre>
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540
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"></span>
</pre>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>Mapping of activators onto Principle Components"</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/pca_conditions.png" % dir</span></span>
</pre>
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543
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC543" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<BR>pca_conditions.png:<BR><img src='%s'>" % newfname</span></span>
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544
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"></span>
</pre>
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545
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/condition_PCs.png" % dir</span></span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>condition_PCs.png:<BR><img src='%s'>" % newfname</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># newfname = "%s/varimax.png" % dir</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "<P>varimax.png:<BR><img src='%s'>" % newfname</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print "</BODY></HTML>"</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_pdf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">html_content</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;">to_html</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</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_file</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="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"{0}.html"</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;">file_name</span><span class="p">),</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">html_content</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">pdfkit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_string</span><span class="p">(</span><span class="n" style="color: #333;">html_content</span><span class="p">,</span> <span class="s" style="color: #d14;">"{0}.pdf"</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;">file_name</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC560" 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>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="python"><span class="s" style="color: #d14;"> python </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s multitnseq <ref.fna> <ref.prot_table> <combined_wig> <samples_metadata> <conditions_metadata> <output_filename> [-K n] [-D n] [-debatch] [-stdnorm]</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="python"><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;">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;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"MultiTnseq example."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#248de6f0e54431894dd74588d32165ead2015eb5"><strong>src/pytransit/analysis/multitnseq_helpers.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">rpy2.robjects</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">globalenv</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">def_r_clustering</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> r_clustering = function(data_filename, K, D) {</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;"> # input: temp_LFCs.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;"> data = read.table(data_filename,head=T,sep='</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">')</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;"> lfcs = data[,3:length(colnames(data))]</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;"> labels = paste(data$Rv,'/',data$Gene,sep="")</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;"> rownames(lfcs) = labels</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;"> R = length(rownames(lfcs)) # genes</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;"> C = length(colnames(lfcs)) # conditions</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;"> library(corrplot)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "lfcs_boxplot.png"</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=300+15*C,height=500)</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> boxplot(lfcs,las=2,ylab="log2 fold change of genes (relative to the median)")</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> km = kmeans(lfcs,K)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> clusters = km$cluster</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> write.table(data.frame(lfcs,clust=clusters),"temp_clust.txt", sep='</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">', quote=F)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> pca = prcomp(t(lfcs))</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> library(MASS)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> mat = as.matrix(lfcs)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> ldapca = lda(clusters~.,lfcs)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> X = mat </span><span class="si" style="color: #d14;">%*% </span><span class="s" style="color: #d14;">ldapca$scaling[,1]</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> Y = mat </span><span class="si" style="color: #d14;">%*% </span><span class="s" style="color: #d14;">ldapca$scaling[,2]</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "pca_genes.png"</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=1000,height=1000)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> plot(X,Y,pch=20)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> text(X,Y,label=labels,adj=c(0.5,1.5),col=clusters)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> actpca = prcomp(lfcs,center=TRUE,scale=TRUE)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "pca_conditions.png"</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=500,height=500)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> plot(actpca$rotation[,1:2],pch=20)#,xlim=c(-1,1),ylim=c(-1,1))</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> text(actpca$rotation[,1:2],label=colnames(lfcs),adj=c(0.5,1.5),cex.lab=1.5)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> print(length(lfcs[,1]))</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> hc = hclust(dist(lfcs),method="ward.D2")</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> print("****hclust_genes****")</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> print(hc)</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "hclust_genes.png"</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=300+15*R,height=600)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> plot(hc)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> K2 = max(2,min(K,max(hc$height)))</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> rect.hclust(hc,k=K2,border='red')</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> hc = hclust(dist(t(lfcs)),method="ward.D2")</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;"> print("****hclust_conditions****")</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> print(hc)</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "hclust_conditions.png"</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=300+15*C,height=600)</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> # plot(hc)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> # D2 = max(2,min(D,C-1))</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"><span class="s" style="color: #d14;"> # rect.hclust(hc,k=D2,border='red')</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> # dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "cluster_opt.png"</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname)</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;"> library(factoextra)</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;"> fviz_nbclust(lfcs, kmeans, method = "wss",k.max=30) # or silhouette or gap_stat</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> #fviz_nbclust ( lfcs, kmeans, method = "wss",k.max=30)+geom_hline ( yintercept=52 )+geom_vline(xintercept=10)</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> ####################################################</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> # required factoextra and corrplot libraries</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> var = get_pca_var(actpca) </span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "condition_PCs.png"</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=1000,height=1000)</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> corrplot(var$cor,main="Principle Components",mar=c(1,1,1,1))</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> S = diag(actpca$sdev,D,D)</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;"> rawLoadings = actpca$rotation[,1:D] </span><span class="si" style="color: #d14;">%*% </span><span class="s" style="color: #d14;">S</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> vmax = varimax(rawLoadings)</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> rotatedLoadings = vmax$loadings</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;"> rotatedScores = scale(actpca$x[,1:D]) </span><span class="si" style="color: #d14;">%*% </span><span class="s" style="color: #d14;">vmax$rotmat</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> # https://stats.stackexchange.com/questions/59213/how-to-compute-varimax-rotated-principal-components-in-r</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> # scores = U.S = X.V = actpca$x = scale(lfcs) </span><span class="si" style="color: #d14;">%*% </span><span class="s" style="color: #d14;">actpca$rotation</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> combined_transform = (actpca$rotation[,1:D] </span><span class="si" style="color: #d14;">%*% </span><span class="s" style="color: #d14;">S) </span><span class="si" style="color: #d14;">%*% </span><span class="s" style="color: #d14;">vmax$rotmat</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> # vmax$loadings is same as combined_transform, but with abs(vals)<0.1 blanked out</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> write.table(round(combined_transform,6),"varimax_loadings.txt",sep='</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">',quote=F)</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "varimax.png"</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=800,height=800)</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> corrplot(rotatedLoadings,main="Varimax loadings",mar=c(1,1,1,1)) </span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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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="s" style="color: #d14;"> scores = rotatedScores</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> colnames(scores) = paste("score",seq(1:D),sep="")</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> squares = scores*scores</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;"> ss = apply(squares,1,sum)</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> cos2 = squares/ss</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> best = as.matrix(apply(cos2,1,max))</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> assoc = cos2*sign(scores)</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> colnames(assoc) = paste("assoc",seq(1:D),sep="")</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> # # generate null distribution for cos2 to closest axis</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> # </span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;"> # library(MASS)</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> # SAMPLES = 10000</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"><span class="s" style="color: #d14;"> # sample = mvrnorm(n=SAMPLES,mu=rep(0,D),Sigma=diag(D))</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;"> # # no need to apply Varimax rotation</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> # squares = sample*sample</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> # ss = apply(squares,1,sum)</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;"> # Xcos2 = squares/ss</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> # Xbest = as.matrix(apply(Xcos2,1,max))</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> # #distn = ecdf(best)</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> # pvals = apply(best,1,function (x) { length(Xbest[Xbest>=x]) })</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;"> # pvals = pvals/SAMPLES</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> # padj = p.adjust(pvals,method="BH")</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> #res = data.frame(data,scores,assoc,best,pvals,padj)</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> res = data.frame(data,scores,assoc)</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> write.table(format(res,digits=3,scientific=F), "temp_scores.txt",sep='</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">',quote=F,row.names=F)</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">globalenv</span><span class="p">[</span><span class="s" style="color: #d14;">'r_clustering'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">def_r_samples_corrplot</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> r_samples_corrplot = function(data_filename) {</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;"> data = read.table(data_filename, sep='</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">',head=T)</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;"> vals = as.matrix(data[,4:length(colnames(data))])</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;"> N = length(colnames(vals))</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;"> library(corrplot)</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "samples_corrplot.png"</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=300+20*N,height=300+20*N)</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;"> #corrplot(cor(vals)) # among TAsites (not good)</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> TAsites = aggregate ( coord~ORF,data=data,length)</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;"> colnames(TAsites) = c("ORF","sites")</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"> temp = aggregate(vals,by=list(data$ORF),FUN=mean)</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> corrplot(cor(temp[TAsites$sites>=10,2:length(colnames(temp))]))</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> }'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">globalenv</span><span class="p">[</span><span class="s" style="color: #d14;">'r_samples_corrplot'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">def_r_conditions_corrplot</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;"> r_conditions_corrplot = function(data_filename) {</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> data = read.table(data_filename, sep='</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">', head=T)</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;"> vals = as.matrix(data[,3:length(colnames(data))])</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"><span class="s" style="color: #d14;"> N = length(colnames(vals))</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> library(corrplot)</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> png("conditions_corrplot.png", width=20*N+300, height=20*N+300)</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> corrplot(cor(vals))</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">globalenv</span><span class="p">[</span><span class="s" style="color: #d14;">'r_conditions_corrplot'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">def_r_make_heatmap</span><span class="p">():</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"><span class="s" style="color: #d14;"> r_make_heatmap = function(data_filename) {</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"><span class="s" style="color: #d14;"> data = read.table(data_filename, head=T, sep='</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">')</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"><span class="s" style="color: #d14;"> lfcs = as.matrix(data[,3:length(colnames(data))])</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"><span class="s" style="color: #d14;"> labels = paste(data$Rv,'/',data$Gene,sep="")</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;"> rownames(lfcs) = labels</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"><span class="s" style="color: #d14;"> library(corrplot)</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;"> library(RColorBrewer)</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;"> library(gplots)</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"><span class="s" style="color: #d14;"> # Red for down regulated, green for upregulated. </span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"><span class="s" style="color: #d14;"> redgreen <- function(n) { c( hsv(h=0/6, v=seq(1,0,length=n/2) ), hsv(h=2/6, v=seq(0,1,length=n/2) ), ) }</span></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"><span class="s" style="color: #d14;"> colors <- colorRampPalette(c("red", "white", "green"))(n = 1000)</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"><span class="s" style="color: #d14;"> C = length(colnames(lfcs))</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;"> R = length(rownames(lfcs))</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"><span class="s" style="color: #d14;"> W = 300+C*30</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;"> H = 300+R*15</span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> fname = "heatmap.png"</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;"> png(fname,width=W,height=H)</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> #par(oma=c(10,1,1,10)) # b,l,t,r; units="lines of space"</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> heatmap.2(lfcs,col=colors,margin=c(12,12),lwid=c(1,7),lhei=c(1,7),trace="none",cexCol=1.4,cexRow=1.4) # make sure white=0</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"> dev.off()</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">globalenv</span><span class="p">[</span><span class="s" style="color: #d14;">'r_make_heatmap'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"></span></pre>
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<li id="8e11d91610ba5cb2818cb8b617ccef1599a952fd">
<a href="https://salsa.debian.org/med-team/tnseq-transit/commit/cad37841e08d266124e4f6f971a2e2aad871a44c#8e11d91610ba5cb2818cb8b617ccef1599a952fd"><strong>src/pytransit/analysis/pathway_enrichment.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">@@ -177,13 +177,13 @@ class GSEAMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC177" 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;">dict_n</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">dict_k</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">dict_n</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <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;">I</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"parameters"</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">k</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">n</span></span><span class="p">),</span><span class="s" style="color: #d14;">"p-value"</span><span class="p">:</span> <span class="n" style="color: #333;">hypergeom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">M</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 class="s" style="color: #d14;">"Intersection"</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="LC180" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"parameters"</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">n</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">k</span></span><span class="p">),</span><span class="s" style="color: #d14;">"p-value"</span><span class="p">:</span> <span class="n" style="color: #333;">hypergeom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">M</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 class="s" style="color: #d14;">"Intersection"</span><span class="p">:</span><span class="n" style="color: #333;">I</span><span class="p">}</span></span>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" 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;">padjustForHypergeom</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">padjustForHypergeom</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">result</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">pvalues</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="s" style="color: #d14;">"p-value"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">]</span></span>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multitest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fdrcorrection</span><span class="p">(</span><span class="n" style="color: #333;">pvalues</span><span class="p">,</span> <span class="n" style="color: #333;">alpha</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.05</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'indep'</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;"> <span id="LC189" 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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">)):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(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="357" style="width: 35px; color: rgba(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">@@ -357,7 +357,7 @@ class GSEAMethod(base.SingleConditionMethod):</td>
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357
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<pre style="margin: 0;"> <span id="LC357" 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>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">padjustTest</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">test</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">test</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">test</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC361" 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;">test</span><span class="p">[</span><span class="n" style="color: #333;">k</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;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">]</span></span>
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multitest</span><span class="o" style="font-weight: 600;">.</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="n" style="color: #333;">alpha</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.05</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'indep'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC363" 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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">)):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="453" style="width: 35px; color: rgba(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="453" style="width: 35px; color: rgba(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">@@ -453,7 +453,7 @@ class GSEAMethod(base.SingleConditionMethod):</td>
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453
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="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;">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="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;">columns</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC454" 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;">saveExit</span><span class="p">(</span><span class="n" style="color: #333;">gseaVal</span><span class="p">,</span><span class="n" style="color: #333;">PathDict</span><span class="p">,</span><span class="n" style="color: #333;">rank</span><span class="p">,</span><span class="n" style="color: #333;">ORFNameDict</span><span class="p">,</span><span class="n" style="color: #333;">DESCR</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"HYPE"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"cat id<span class="idiff left right"> </span>descr"</span><span class="p">,</span><span class="s" style="color: #d14;">"Total genes"</span><span class="p">,</span><span class="s" style="color: #d14;">"Total in intersection"</span><span class="p">,</span><span class="s" style="color: #d14;">"pval"</span><span class="p">,</span><span class="s" style="color: #d14;">"padj"</span><span class="p">,</span><span class="s" style="color: #d14;">"genes in intersection"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"cat id<span class="idiff left">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>descr"</span><span class="p">,</span><span class="s" style="color: #d14;">"Total genes"</span><span class="p">,</span><span class="s" style="color: #d14;">"Total in intersection"</span><span class="p">,</span><span class="s" style="color: #d14;">"pval"</span><span class="p">,</span><span class="s" style="color: #d14;">"padj"</span><span class="p">,</span><span class="s" style="color: #d14;">"genes in intersection"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC457" 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;">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="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;">columns</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC458" 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;">saveHyperGeometricTest</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span><span class="n" style="color: #333;">ORFNameDict</span><span class="p">,</span><span class="n" style="color: #333;">DESCR</span><span class="p">)</span></span>
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459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"GSEA-Z"</span><span class="p">:</span></span>
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