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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/tnseq-transit">Debian Med / tnseq-transit</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/3b803d0613a70d5cdb6711783eca45db9e55fc51">3b803d06</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-29T02:47:18+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/290ac4e119847a16a800df4e52b7ff900f739588">290ac4e1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-29T02:49:24+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2.0'
Update to upstream version '3.2.0'
with Debian dir 70023e8dfdb58da65004e0aa1110af083f1df406</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/960097a9170f1d03b8b46705d8761b30742e1160">960097a9</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-29T02:54:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
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<h4>17 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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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="#64ebb63bfd04d60140d82fdcdf340e3e2e150526">
src/pytransit/analysis/corrplot.py
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<li class="file-stats">
<a href="#8f7b871a787b5d5c5b3a11bed95337c59a510906">
src/pytransit/analysis/gi.py
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<li class="file-stats">
<a href="#79133d97a873c0457c3b9203ce6b36f131c0e882">
src/pytransit/analysis/heatmap.py
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<li class="file-stats">
<a href="#8e11d91610ba5cb2818cb8b617ccef1599a952fd">
src/pytransit/analysis/pathway_enrichment.py
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<li class="file-stats">
<a href="#b1616bd66829b174aefbf8f12356d430430acbad">
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src/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt
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<li class="file-stats">
<a href="#0517df3fd9965095cce6712ccae8ceb6727b7be8">
src/pytransit/data/H37Rv_COG_roles.dat
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<li class="file-stats">
<a href="#b09ef31d42e430ff42b72b80215384a2ddaf2f06">
src/pytransit/data/H37Rv_sanger_roles.dat
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<li class="file-stats">
<a href="#fc29d9a492f58c9988bd4e693a51249520e29065">
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src/pytransit/data/gene_ontology.1_2.3-11-18.obo
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<a href="#32ef3fe57b770a4ab15bcda79774a4789b923284">
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src/pytransit/doc/source/_images/genetic_interaction_types.png
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<li class="file-stats">
<a href="#e4c47efb9db43431093096e67f5aab587b257ff4">
src/pytransit/doc/source/transit_methods.rst
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<li class="file-stats">
<a href="#1e85e527482a20741c2118e954cce9ba93cbe299">
src/pytransit/export/mean_counts.py
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<li class="file-stats">
<a href="#320e7dcd48d9a3178f02350c2087027bb27bd8d7">
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src/pytransit/genomes/genomes.html~
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<li class="file-stats">
<a href="#d0edb611a89a0dab9d0dc046d324f550b89d3d03">
src/pytransit/transit_gui.py
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<li class="file-stats">
<a href="#e5b0cbf3e2b7da50e81a6a816bad4db5f931e6ca">
<span class="new-file">
+
tests/H37Rv.fna
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">All notable changes to this project will be documented in this file.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.0 2020-10-26</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p"> -</span> improvements to pathway_enrichment analysis</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p"> -</span> added '--ranking' flag for GSEA to sort genes based on LFC or SLPV</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p"> -</span> implemented Ontologizer method (-M ONT), which works better for GO terms</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p"> -</span> updated auxilliary files in transit data directory for different systems of functional categories (COG, Sanger, GO)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p"> -</span> added '-signif' flag to GI (Genetic Interaction analysis) (options: HDI, prob, BFDR, FWER)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> -</span> updated description of methods for determining significant interactions in documentation</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p"> -</span> various improvements to other methods, including corrplot and heatmap</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.1.0 2020-03-08</span></span>
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(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="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p"> -</span> added 'corrplot' and 'heatmap' commands</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tnseq-transit (3.2.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version 3.2.0</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Thu, 29 Oct 2020 02:49:44 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">tnseq-transit (3.1.0-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4"><strong>src/pytransit/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,6 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"transit_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tnseq_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"norm_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stat_tools"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.<span class="idiff left right">1</span>.0"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.<span class="idiff left right">2</span>.0"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[TRANSIT]"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#64ebb63bfd04d60140d82fdcdf340e3e2e150526"><strong>src/pytransit/analysis/corrplot.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">@@ -154,6 +154,8 @@ class CorrplotMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">genenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"%s/%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">w</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;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC155" 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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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"Mean_"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">headers</span><span class="p">]</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">replace</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 class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">headers</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># because of R conversion</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"X"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">if</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="n" style="color: #333;">isdigit</span><span class="p">()</span> <span class="k" style="font-weight: 600;">else</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;">headers</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># because R prepends 'X' to column names starting with a digit</span></span>
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157
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159
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<pre style="margin: 0;"> <span id="LC159" 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;">col</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;">headers</span><span class="p">):</span> <span class="nb" style="color: #0086b3;">hash</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FloatVector</span><span class="p">([</span><span class="n" style="color: #333;">x</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;">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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158
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="nb" style="color: #0086b3;">hash</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># can't figure out how to set rownames</span></span>
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159
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>
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<li id="8f7b871a787b5d5c5b3a11bed95337c59a510906">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#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">@@ -22,7 +22,7 @@ import math</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>
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<pre style="margin: 0;"> <span id="LC23" 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="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy.stats</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span><span class="idiff left right"> </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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pytransit.analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">base</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytransit</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +44,7 @@ NOTE: This method requires 4 groups of datasets. Use the main interface to add d</td>
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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 class="s" style="color: #d14;">"himar1"</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<span class="idiff left right"> (BFDR)</span>"</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="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"</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="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GIAnalysis</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">TransitAnalysis</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,7 +143,7 @@ class GIGUI(base.AnalysisGUI):</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Zeros Check</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">giZeroCheckBox</span><span class="p">,</span> <span class="n" style="color: #333;">zeroSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineCheckBox</span><span class="p">(</span><span class="n" style="color: #333;">giPanel</span><span class="p">,</span> <span class="n" style="color: #333;">labelText</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Include sites with all zeros"</span><span class="p">,</span> <span class="n" style="color: #333;">widgetCheck</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;">widgetSize</span><span class="o" style="font-weight: 600;">=</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="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">tooltipText</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Includes sites that are empty (zero) ac<span class="idiff left right">c</span>ross all datasets. Unchecking this may be useful for tn5 datasets, where all nucleotides are possible insertion sites and will have a large number of empty sites (significantly slowing down computation and affecting estimates)."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wxobj</span><span class="p">.</span><span class="n" style="color: #333;">giZeroCheckBox</span><span class="p">,</span> <span class="n" style="color: #333;">zeroSizer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">defineCheckBox</span><span class="p">(</span><span class="n" style="color: #333;">giPanel</span><span class="p">,</span> <span class="n" style="color: #333;">labelText</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Include sites with all zeros"</span><span class="p">,</span> <span class="n" style="color: #333;">widgetCheck</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;">widgetSize</span><span class="o" style="font-weight: 600;">=</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="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">tooltipText</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Includes sites that are empty (zero) across all datasets. Unchecking this may be useful for tn5 datasets, where all nucleotides are possible insertion sites and will have a large number of empty sites (significantly slowing down computation and affecting estimates)."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">giSizer</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">zeroSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -474,6 +474,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">normalization</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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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10000</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">rope</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">signif</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"HDI"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">includeZeros</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="LC479" class="line" lang="python"> <span class="n" style="color: #333;">replicates</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Sum"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">LOESS</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -486,8 +487,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="bp" style="color: #999;">self</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;">samples</span></span>
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">includeZeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">includeZeros</span></span>
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488
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rope</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rope</span></span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doBFDR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="c1" style="color: #998; font-style: italic;"># TRI</span></span>
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490
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doFWER</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="c1" style="color: #998; font-style: italic;"># TRI</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">signif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">signif</span></span>
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491
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">NTerminus</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NTerminus</span></span>
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492
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">CTerminus</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CTerminus</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="558" style="width: 35px; color: rgba(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">@@ -558,6 +558,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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558
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<pre style="margin: 0;"> <span id="LC558" 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;">output_path</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">output_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"> <span class="n" style="color: #333;">signif</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"HDI"</span> <span class="c1" style="color: #998; font-style: italic;"># need to add choice for this to the GUI</span></span>
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"></span>
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562
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<pre style="margin: 0;"> <span id="LC563" 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;">ctrldataA</span><span class="p">,</span></span>
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563
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="n" style="color: #333;">ctrldataB</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="569" style="width: 35px; color: rgba(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">@@ -568,6 +569,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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568
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">normalization</span><span class="p">,</span></span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">samples</span><span class="p">,</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">rope</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">signif</span><span class="p">,</span></span>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">includeZeros</span><span class="p">,</span></span>
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">replicates</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">LOESS</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -600,10 +602,10 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="python"> <span class="n" style="color: #333;">normalization</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"n"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTR"</span><span class="p">)</span></span>
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601
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"s"</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">))</span></span>
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">rope</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;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-rope"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.5</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># fixed! changed int to float</span></span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">signif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"signif"</span><span class="p">,</span><span class="s" style="color: #d14;">"HDI"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Sum"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">includeZeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"iz"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">LOESS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"l"</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="LC610" class="line" lang="python"> <span class="n" style="color: #333;">ignoreCodon</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="LC611" class="line" lang="python"> <span class="n" style="color: #333;">NTerminus</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;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"iN"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -618,6 +620,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> <span class="n" style="color: #333;">normalization</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"> <span class="n" style="color: #333;">samples</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">rope</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">signif</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"> <span class="n" style="color: #333;">includeZeros</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">replicates</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"> <span class="n" style="color: #333;">LOESS</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="677" style="width: 35px; color: rgba(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">@@ -674,7 +677,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">var_list_b2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Base priors on empirical observations ac<span class="idiff left right">c</span>ross genes.</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Base priors on empirical observations across genes.</span></span>
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<pre style="margin: 0;"> <span id="LC681" 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="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">G_A1</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene</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="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">A1_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G_A1</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">orf</span><span class="p">].</span><span class="n" style="color: #333;">reads</span><span class="p">.</span><span class="n" style="color: #333;">flatten</span><span class="p">()</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -764,7 +767,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="python"> <span class="n" style="color: #333;">mean_logFC_B</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">logFC_B_post</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="python"> <span class="n" style="color: #333;">mean_delta_logFC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">delta_logFC_post</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Is HDI significantly different than ROPE?</span></span>
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Is HDI significantly different than ROPE?<span class="idiff left right"> (i.e. no overlap)</span></span></span>
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"> <span class="n" style="color: #333;">not_HDI_overlap_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l_delta_logFC</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rope</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">u_delta_logFC</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rope</span></span>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Probability of posterior overlaping with ROPE</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -816,25 +819,35 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message_inplace</span><span class="p">(</span><span class="s" style="color: #d14;">"Running Export Method... %1.1f%%"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mf" style="color: #099;">100.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">/</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="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="python"> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for HDI, maybe I should sort on abs(mean_delta_logFC); however, need to sort by prob to calculate BFDR</span></span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="python"> <span class="n" style="color: #333;">probcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="c1" style="color: #998; font-style: italic;"># probROPEs</span></span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">probcol</span><span class="p">])</span> </span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="python"> <span class="n" style="color: #333;">sortedprobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">probcol</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;">data</span><span class="p">])</span> </span>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># BFDR method: Newton M.A., Noueiry A., Sarkar D., Ahlquist P. (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics, 5:155–176.</span></span>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">doBFDR</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">doFWER</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">postprob</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numpy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">postprob</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">postprob</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sort</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="python"> <span class="n" style="color: #333;">bfdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">cumsum</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">postprob</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">numpy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">arange</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">postprob</span></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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<pre style="margin: 0;">-<span id="LC825" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bfdr</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">signif</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="s" style="color: #d14;"><span class="idiff right">"BFDR"</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">sortedprobs</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numpy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sortedprobs</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#sortedprobs.sort() # why, since already sorted?</span></span></span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="python"> <span class="n" style="color: #333;">bfdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">cumsum</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sortedprobs</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">numpy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">arange</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">sortedprobs</span></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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<pre style="margin: 0;">+<span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bfdr</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># should be same order as sorted above by probROPE</span></span></span>
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BFDR"</span></span>
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">doFWER</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="python"> <span class="n" style="color: #333;">fwer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FWER_Bayes</span><span class="p">(</span><span class="n" style="color: #333;">postprob</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="n" style="color: #333;">fwer</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">signif</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"FWER"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="python"> <span class="n" style="color: #333;">fwer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat_tools</span><span class="p">.</span><span class="n" style="color: #333;">FWER_Bayes</span><span class="p">(</span><span class="n" style="color: #333;">sortedprobs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#fwer.sort() # should not need this if monotonic</span></span>
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fwer</span></span>
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FWER"</span></span>
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If not using adjustment for classification, sort correctly</span></span>
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doBFDR</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doFWER</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="python"> <span class="n" style="color: #333;">sorted_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">argsort</span><span class="p">([</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</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;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">adjusted_prob</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ii</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sorted_index</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC837" 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="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ii</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sorted_index</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sortedprobs</span></span>
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="python"> <span class="n" style="color: #333;">adjusted_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"un"</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># should I stable-sort by overlap_bit?</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># sorted_index = numpy.argsort([d[-1] for d in data])[::-1][:len(data)]</span></span>
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># adjusted_prob = [adjusted_prob[ii] for ii in sorted_index]</span></span>
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># data = [data[ii] for ii in sorted_index]</span></span>
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="python"></span>
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -848,37 +861,40 @@ class GIMethod(base.QuadConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Console: python3 %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="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python"></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">now</span><span class="p">[:</span><span class="n" style="color: #333;">now</span><span class="p">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)]</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Date: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">now</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#self.output.write("#Runtime: %s s\n" % (time.time() - start_time))</span></span>
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python"></span>
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Control Data-A: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldataA</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)))</span></span>
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Control Data-B: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldataB</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)))</span></span>
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Experimental Data-A: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">expdataA</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)))</span></span>
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Experimental Data-B: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">expdataB</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)))</span></span>
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Annotation path: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Time: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start_time</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</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="p">.</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="LC859" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#ROPE=%s, method for significance=%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rope</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">signif</span><span class="p">))</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#self.output.write("#%s\n" % "\t".join(columns))</span></span>
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doBFDR</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doFWER</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Significant interactions are those whose adjusted probability of the delta-logFC falling within ROPE is < 0.05 (Adjusted using %s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">adjusted_label</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Significant interactions are those genes whose delta-logFC HDI does not overlap the ROPE</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="LC865" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</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;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">signif</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"HDI"</span><span class="p">:</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Significant interactions are those genes whose delta-logFC HDI does not overlap the ROPE</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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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">signif</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"prob BDFR FWER"</span><span class="p">:</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Significant interactions are those whose %s-adjusted probability of the delta-logFC falling within ROPE is < 0.05.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">adjusted_label</span><span class="p">))</span></span>
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866
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write column names</span></span>
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Name</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Number of TA Sites</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain A Condition 1)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain A Condition 2)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain B Condition 1)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain B Condition 2)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean logFC (Strain A)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean logFC (Strain B) </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean delta logFC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Lower Bound delta logFC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Upper Bound delta logFC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">Prob. of delta-logFC being within ROPE</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">Adjusted Probability (%s)</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">Is HDI outside ROPE?</span></span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Type of Interaction</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="n" style="color: #333;">adjusted_label</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write column names<span class="idiff left right"> (redundant with self.columns)</span></span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Name</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Number of TA Sites</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain A Condition 1)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain A Condition 2)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain B Condition 1)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean count (Strain B Condition 2)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean logFC (Strain A)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean logFC (Strain B) </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mean delta logFC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Lower Bound delta logFC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Upper Bound delta logFC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">Is HDI outside ROPE?</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">Prob. of delta-logFC being within ROPE</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">%s-Adjusted Probability</span></span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Type of Interaction</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="n" style="color: #333;">adjusted_label</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python"></span>
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870
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write gene results</span></span>
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887
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<pre style="margin: 0;"> <span id="LC887" 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;">row</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;">data</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#1 2 3 4 5 6 7 8 9 10 11 12 13 14</span></span>
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873
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">orf</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muA1_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muA2_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muB1_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muB2_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_logFC_A</span><span class="p">,</span> <span class="n" style="color: #333;">mean_logFC_B</span><span class="p">,</span> <span class="n" style="color: #333;">mean_delta_logFC</span><span class="p">,</span> <span class="n" style="color: #333;">l_delta_logFC</span><span class="p">,</span> <span class="n" style="color: #333;">u_delta_logFC</span><span class="p">,</span> <span class="n" style="color: #333;">probROPE</span><span class="p">,</span> <span class="n" style="color: #333;">not_HDI_overlap_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span></span>
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">type_of_interaction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"No Interaction"</span></span></span>
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875
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">doBFDR</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">doFWER</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">adjusted_prob</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.05</span></span><span class="p"><span class="idiff right">):</span></span></span>
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876
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">type_of_interaction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">classify_interaction</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mean_delta_logFC</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mean_logFC_B</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mean_logFC_A</span></span><span class="p"><span class="idiff right">)</span></span></span>
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877
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">elif</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">doBFDR</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">doFWER</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">not_HDI_overlap_bit</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">type_of_interaction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">classify_interaction</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mean_delta_logFC</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mean_logFC_B</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mean_logFC_A</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="python"> <span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">#1 2 3 4 5 6 7 8 9 10 11 12 13 14</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="python"> <span class="n" style="color: #333;">orf</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muA1_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muA2_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muB1_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_muB2_post</span><span class="p">,</span> <span class="n" style="color: #333;">mean_logFC_A</span><span class="p">,</span> <span class="n" style="color: #333;">mean_logFC_B</span><span class="p">,</span> <span class="n" style="color: #333;">mean_delta_logFC</span><span class="p">,</span> <span class="n" style="color: #333;">l_delta_logFC</span><span class="p">,</span> <span class="n" style="color: #333;">u_delta_logFC</span><span class="p">,</span> <span class="n" style="color: #333;">probROPE</span><span class="p">,</span> <span class="n" style="color: #333;">not_HDI_overlap_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">interaction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">classify_interaction</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mean_delta_logFC</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mean_logFC_B</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mean_logFC_A</span></span><span class="p"><span class="idiff right">)</span></span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">type_of_interaction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"No Interaction"</span></span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">signif</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"prob BFDR FWER"</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">adjusted_prob</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.05</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">type_of_interaction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">interaction</span></span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">signif</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="s" style="color: #d14;"><span class="idiff">"HDI"</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">not_HDI_overlap_bit</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">type_of_interaction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">interaction</span></span></span>
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879
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="python"></span>
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880
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">new_row</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">row</span></span><span class="p"><span class="idiff">[:</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">adjusted_prob</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">not_HDI_overlap_bit</span></span><span class="p">,</span> <span class="n" style="color: #333;">type_of_interaction</span><span class="p">])</span></span>
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881
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="python"> <span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">output</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">write</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"%s</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%s</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%d</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.8f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.8f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">%s</span></span><span class="se" style="color: #d14;">\t</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="n" style="color: #333;">new_row</span><span class="p">)</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">new_row</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">row</span></span><span class="p"><span class="idiff">[:</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">not_HDI_overlap_bit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">probROPE</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">adjusted_prob</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">type_of_interaction</span><span class="p">])</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">output</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">write</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"%s</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%s</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%d</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.2f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%s</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">%1.8f</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">%1.8f</span></span><span class="se" style="color: #d14;">\t</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="n" style="color: #333;">new_row</span><span class="p">)</span></span>
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882
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="python"></span>
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Adding File: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -907,16 +923,24 @@ class GIMethod(base.QuadConditionMethod):</td>
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907
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923
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="python"><span class="s" style="color: #d14;"> GI performs a comparison among 4 groups of datasets, strain A and B assessed in conditions 1 and 2 (e.g. control vs treatment).</span></span>
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908
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="python"><span class="s" style="color: #d14;"> It looks for interactions where the response to the treatment (i.e. effect on insertion counts) depends on the strain (output variable: delta_LFC).</span></span>
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909
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="python"><span class="s" style="color: #d14;"> Provide replicates in each group as a comma-separated list of wig files.</span></span>
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910
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="python"><span class="s" style="color: #d14;"> Significant interactions are those with "HDI outside ROPE?"=TRUE, and all genes are sorted by significance using BFDR."</span></span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="python"><span class="s" style="color: #d14;"> HDI is highest density interval for posterior distribution of delta_LFC, which is like a confidence interval on difference of slopes.</span></span>
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="python"><span class="s" style="color: #d14;"> Genes are sorted by probability of HDI overlapping with ROPE. (genes with the highest abs(mean_delta_logFC) are near the top, approximately)</span></span>
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="python"><span class="s" style="color: #d14;"> Significant genes are indicated by 'Type of Interaction' column (No Interaction, Aggravating, Alleviating, Suppressive).</span></span>
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="python"><span class="s" style="color: #d14;"> By default, hits are defined as "Is HDI outside of ROPE?"=TRUE (i.e. non-overlap of delta_LFC posterior distritbuion with Region of Probably Equivalence around 0)</span></span>
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="python"><span class="s" style="color: #d14;"> Alternative methods for significance: use -signif flag with prob, BFDR, or FWER. These affect 'Type of Interaction' (i.e. which genes are labeled 'No Interaction')</span></span>
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="python"></span>
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912
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="python"><span class="s" style="color: #d14;"> Optional Arguments:</span></span>
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913
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="python"><span class="s" style="color: #d14;"> -s <integer> := Number of samples. Default: -s 10000</span></span>
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914
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="python"><span class="s" style="color: #d14;"> --rope <float> := Region of Practical Equivalence. Area around 0 (i.e. 0 +/- ROPE) that is NOT of interest. Can be thought of similar to the area of the null-hypothesis. Default: --rope 0.5</span></span>
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="python"><span class="s" style="color: #d14;"> -n <string> := Normalization method. Default: -n TTR</span></span>
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="python"><span class="s" style="color: #d14;"> -iz := Include rows with zero ac<span class="idiff left right">c</span>ross conditions.</span></span>
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="python"><span class="s" style="color: #d14;"> -iz := Include rows with zero across conditions.</span></span>
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937
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<pre style="margin: 0;"> <span id="LC937" class="line" lang="python"><span class="s" style="color: #d14;"> -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Turned Off.</span></span>
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="python"><span class="s" style="color: #d14;"> -iN <float> := Ignore TAs occuring at given percentage (as integer) of the N terminus. Default: -iN 0</span></span>
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919
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939
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<pre style="margin: 0;"> <span id="LC939" class="line" lang="python"><span class="s" style="color: #d14;"> -iC <float> := Ignore TAs occuring at given percentage (as integer) of the C terminus. Default: -iC 0</span></span>
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="python"><span class="s" style="color: #d14;"> -signif HDI := (default) Significant if HDI does not overlap ROPE; if HDI overlaps ROPE, 'Type of Interaction' is set to 'No Interaction'</span></span>
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="python"><span class="s" style="color: #d14;"> -signif prob := Optionally, significant hits are re-defined based on probability (degree) of overlap of HDI with ROPE, prob<0.05 (no adjustment)</span></span>
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="python"><span class="s" style="color: #d14;"> -signif BFDR := Apply "Bayesian" FDR correction (see doc) to adjust HDI-ROPE overlap probabilities so that significant hits are re-defined as BFDR<0.05</span></span>
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="python"><span class="s" style="color: #d14;"> -signif FWER := Apply "Bayesian" FWER correction (see doc) to adjust HDI-ROPE overlap probabilities so that significant hits are re-defined as FWER<0.05</span></span>
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<pre style="margin: 0;"> <span id="LC944" 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="p">.</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="LC945" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="python"></span>
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<li id="79133d97a873c0457c3b9203ce6b36f131c0e882">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#79133d97a873c0457c3b9203ce6b36f131c0e882"><strong>src/pytransit/analysis/heatmap.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">@@ -102,41 +102,51 @@ class HeatmapMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC103" 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="LC104" 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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<pre style="margin: 0;">+<span id="LC105" 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="p">.</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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<pre style="margin: 0;"> <span id="LC106" 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;">rawargs</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 class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">usage_string</span><span class="p">());</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">rawargs</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="s" style="color: #d14;"><span class="idiff right">"-anova"</span></span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"anova"</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;"><span class="idiff left">rawargs</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="s" style="color: #d14;"><span class="idiff right">"-zinb"</span></span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"zinb"</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">kwargs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"anova"</span></span><span class="p"><span class="idiff">,</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff right">)</span>:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"anova"</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;"><span class="idiff left">kwargs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"zinb"</span></span><span class="p"><span class="idiff">,</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff right">)</span>:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"zinb"</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">usage_string</span><span class="p">());</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">infile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rawargs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rawargs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">infile</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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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">outfile</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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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qval</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;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"qval"</span><span class="p">,</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="LC114" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">topk</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"topk"</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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<pre style="margin: 0;"> <span id="LC115" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">infile</span><span class="p">,</span><span class="n" style="color: #333;">outfile</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span 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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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assume first non-comment line is header; samples are </span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">"anova"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">"zinb"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"filetype not recognized: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="p">);</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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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<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="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span><span class="n" style="color: #333;">LFCs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[]</span></span>
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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="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"anova"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"zinb"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</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;"># number of conditions</span></span>
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<pre style="margin: 0;">-<span id="LC122" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">infile</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC123" 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="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="s" style="color: #d14;">'pval'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'padj'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># check for 'pval' for backwards compatibility</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">;</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># keep last comment line as headers</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" 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;">1</span><span class="p">:</span> </span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ANOVA header line has names of conditions, organized as 3+2*n+3 (2 groups (means, LFCs) X n conditions)</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ZINB header line has names of conditions, organized as 3+4*n+3 (4 groups X n conditions)</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"anova"</span><span class="p">:</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nb" style="color: #0086b3;">len</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;">6</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> </span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"zinb"</span><span class="p">:</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">headers</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> </span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">headers</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="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"Mean_"</span><span class="p">,</span><span class="s" style="color: #d14;">""</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;">headers</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span><span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[]</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</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;"># number of conditions</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">infile</span><span class="p">):</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" 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="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="s" style="color: #d14;">'pval'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'padj'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># check for 'pval' for backwards compatibility</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">;</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># keep last comment line as headers</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assume first non-comment line is header</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" 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;">1</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ANOVA header line has names of conditions, organized as 3+2*n+3 (2 groups (means, LFCs) X n conditions)</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ZINB header line has names of conditions, organized as 3+4*n+3 (4 groups X n conditions)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"anova"</span><span class="p">:</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nb" style="color: #0086b3;">len</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;">6</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"zinb"</span><span class="p">:</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">headers</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">headers</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="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"Mean_"</span><span class="p">,</span><span class="s" style="color: #d14;">""</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;">headers</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">lfcs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</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;">w</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="p">]]</span> <span class="c1" style="color: #998; font-style: italic;"># take just the columns of means</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">qval</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;">w</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qval</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;">data</span><span class="p">.</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="n" style="color: #333;">LFCs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lfcs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"filetype not recognized: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="p">);</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"heatmap based on %s genes"</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;">LFCs</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">.</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="n" style="color: #333;">lfcs</span><span class="p">,</span><span class="n" style="color: #333;">qval</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">genenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"%s/%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">w</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;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="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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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">hits</span><span class="p">,</span><span class="n" style="color: #333;">LFCs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[]</span></span>
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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;">k</span><span class="p">,(</span><span class="n" style="color: #333;">w</span><span class="p">,</span><span class="n" style="color: #333;">lfcs</span><span class="p">,</span><span class="n" style="color: #333;">qval</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;">data</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">topk</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">qval</span><span class="o" style="font-weight: 600;"><</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qval</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">topk</span><span class="o" style="font-weight: 600;">!=-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">topk</span><span class="p">):</span> <span class="n" style="color: #333;">hits</span><span class="p">.</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="n" style="color: #333;">LFCs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lfcs</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>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"heatmap based on %s genes"</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;">hits</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">genenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"%s/%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">w</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;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hits</span><span class="p">]</span></span>
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140
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150
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<pre style="margin: 0;"> <span id="LC150" 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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141
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"Mean_"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">headers</span><span class="p">]</span></span>
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142
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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;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">col</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;">headers</span><span class="p">):</span> <span class="nb" style="color: #0086b3;">hash</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FloatVector</span><span class="p">([</span><span class="n" style="color: #333;">x</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;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">LFCs</span><span class="p">])</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -167,8 +177,7 @@ dev.off()</td>
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"></span>
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168
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178
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<pre style="margin: 0;"> <span id="LC178" 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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169
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179
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<pre style="margin: 0;"> <span id="LC179" 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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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"usage: python3 %s heatmap -anova|-zinb <anova_or_zinb_output> <heatmap.png>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sys</span><span class="p">.</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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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># could add a flag for padj cutoff (or top n most signif genes)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"usage: python3 %s heatmap <anova_or_zinb_output> <heatmap.png> -anova|-zinb [-topk <int>] [-qval <float>]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> note: genes are selected based on qval<0.05 by default"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sys</span><span class="p">.</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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172
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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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173
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"></span>
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174
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183
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<pre style="margin: 0;"> <span id="LC183" 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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<li id="8e11d91610ba5cb2818cb8b617ccef1599a952fd">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#8e11d91610ba5cb2818cb8b617ccef1599a952fd"><strong>src/pytransit/analysis/pathway_enrichment.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" style="width: 35px; color: rgba(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">@@ -79,7 +79,7 @@ class PathwayGUI(base.AnalysisGUI):</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PathwayMethod</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">AnalysisMethod</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC82" 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;">resamplingFile</span><span class="p">,</span><span class="n" style="color: #333;">associationsFile</span><span class="p">,</span><span class="n" style="color: #333;">pathwaysFile</span><span class="p">,</span><span class="n" style="color: #333;">outputFile</span><span class="p">,</span><span class="n" style="color: #333;">method</span><span class="p">,</span><span class="n" style="color: #333;">PC</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 class="idiff left">=</span></span><span class="mi" style="color: #099;"><span class="idiff">10000</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC82" 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;">resamplingFile</span><span class="p">,</span><span class="n" style="color: #333;">associationsFile</span><span class="p">,</span><span class="n" style="color: #333;">pathwaysFile</span><span class="p">,</span><span class="n" style="color: #333;">outputFile</span><span class="p">,</span><span class="n" style="color: #333;">method</span><span class="p">,</span><span class="n" style="color: #333;">PC</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 class="idiff left">perm</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">10000</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">ranking</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"SLPV"</span></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;">base</span><span class="p">.</span><span class="n" style="color: #333;">AnalysisMethod</span><span class="p">.</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="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outputFile</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">),</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># no annotation file</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resamplingFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">resamplingFile</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">associationsFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">associationsFile</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,9 +87,10 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">outputFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputFile</span> </span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.output is the opened file, which will be set in base class</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">method</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">PC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PC</span> <span class="c1" style="color: #998; font-style: italic;"># for F<span class="idiff left right">ISHER</span></span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">N</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">N</span></span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">PC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PC</span> <span class="c1" style="color: #998; font-style: italic;"># for F<span class="idiff left right">ET</span></span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">N<span class="idiff left">perm</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Nperm</span></span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ranking</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ranking</span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="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="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fromGUI</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="p">):</span></span>
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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">@@ -102,37 +103,82 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">associations</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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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">pathways</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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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">output</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="LC105" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"M"</span><span class="p">,</span> <span class="s" style="color: #d14;">"FISHER"</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" 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;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span><span class="p">,</span> <span class="s" style="color: #d14;">"10000"</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA?</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"p"</span><span class="p">,</span><span class="s" style="color: #d14;">"1"</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA?</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">PC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"PC"</span><span class="p">,</span><span class="s" style="color: #d14;">"2"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"M"</span><span class="p">,</span> <span class="s" style="color: #d14;">"FET"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">PC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"PC"</span><span class="p">,</span><span class="s" style="color: #d14;">"2"</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># for FET</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">Nperm</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"Nperm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"10000"</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">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;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"p"</span><span class="p">,</span><span class="s" style="color: #d14;">"0"</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">ranking</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"ranking"</span><span class="p">,</span><span class="s" style="color: #d14;">"SLPV"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># for GSEA</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"F<span class="idiff left right">ISHER</span> GSEA ONT"</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">():</span> </span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"F<span class="idiff left right">ET</span> GSEA ONT"</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">():</span> </span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"error: method %s not recognized"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">method</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">usage_string</span><span class="p">());</span> </span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</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="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"ONT"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"error: Ontologizer is not implemented yet"</span><span class="p">);</span> <span class="n" style="color: #333;">sys</span><span class="p">.</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="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC116" 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;">resamplingFile</span><span class="p">,</span><span class="n" style="color: #333;">associations</span><span class="p">,</span><span class="n" style="color: #333;">pathways</span><span class="p">,</span><span class="n" style="color: #333;">output</span><span class="p">,</span><span class="n" style="color: #333;">method</span><span class="p">,</span><span class="n" style="color: #333;">PC</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PC</span><span class="p">,</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="n" style="color: #333;"><span class="idiff">N</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">p</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">(</span><span class="n" style="color: #333;">resamplingFile</span><span class="p">,</span><span class="n" style="color: #333;">associations</span><span class="p">,</span><span class="n" style="color: #333;">pathways</span><span class="p">,</span><span class="n" style="color: #333;">output</span><span class="p">,</span><span class="n" style="color: #333;">method</span><span class="p">,</span><span class="n" style="color: #333;">PC</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PC</span><span class="p">,</span><span class="n" style="color: #333;">N<span class="idiff left">perm</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">Nperm</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">ranking</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">ranking</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC119" 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="LC120" 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="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""python3 %s pathway_enrichment <resampling_file> <associations> <pathways> <output_file> [-M <FISHER|GSEA|GO>] [-PC <int>]"""</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</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="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""python3 %s pathway_enrichment <resampling_file> <associations> <pathways> <output_file> [-M <FET|GSEA|GO>] [-PC <int>] [-ranking SLPV|LFC] [-p <float>] [-Nperm <int>]</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;">Optional parameters:</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> -M FET|GSEA|ONT: method to use, FET for Fisher's Exact Test (default), GSEA for Gene Set Enrichment Analysis (Subramaniam et al, 2005), or ONT for Ontologizer (Grossman et al, 2007)</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> -ranking (for GSEA): SLPV is signed-log-p-value (default); LFC is log2-fold-change from resampling</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> -p (for GSEA): exponent to use in calculating enrichment score; recommend trying 0 or 1 (as in Subramaniam et al, 2005)</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> -Nperm (for GSEA): number of permutations to simulate for null distribution to determine p-value (default=10000)</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> -PC (for FET): pseudo-counts to use in calculating p-value based on hypergeometric distribution (default=2)</span></span>
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<pre style="margin: 0;">+<span id="LC129" 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="p">.</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="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC131" 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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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Starting Pathway Enrichment Method"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.output in base class should be open by now</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# command: "</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# date: "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">()))</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# command: python3 "</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">now</span><span class="p">[:</span><span class="n" style="color: #333;">now</span><span class="p">.</span><span class="n" style="color: #333;">rfind</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="LC139" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# date: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">now</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# pathway method: "</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">method</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>
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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="bp" style="color: #999;">self</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;">"F<span class="idiff left right">ISHER</span>"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fisher_exact_test</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</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;">"F<span class="idiff left right">ET</span>"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fisher_exact_test</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</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;">"GSEA"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">GSEA</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</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;">"ONT"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">Ontologizer</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;">else</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;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Not a valid method"</span></span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">progress_update</span><span class="p">(</span><span class="s" style="color: #d14;">"Not a valid method"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</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>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">msg</span><span class="p">):</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_resampling_file</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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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">hits</span><span class="p">,</span><span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</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 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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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span><span class="p">:</span> <span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span> <span class="k" style="font-weight: 600;">continue</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;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">genes</span><span class="p">.</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>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">qval</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;">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>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qval</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;">hits</span><span class="p">.</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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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">hits</span><span class="p">,</span><span class="n" style="color: #333;">headers</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assume these are listed as pairs (tab-sep)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return bidirectional hash (genes->[terms], terms->[genes]; each can be one-to-many, hence lists)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_associations</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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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">associations</span> <span class="o" style="font-weight: 600;">=</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="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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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" 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="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># store mappings in both directions</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</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="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">w</span><span class="p">[</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;">1</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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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</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;">associations</span><span class="p">:</span> <span class="n" style="color: #333;">associations</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">associations</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">associations</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"></span>
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174
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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;">read_pathways</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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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">pathways</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" 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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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</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;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">pathways</span><span class="p">[</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</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>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pathways</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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136
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">############### GSEA ######################</span></span>
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137
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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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138
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">makeindex</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">lst</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(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="187" style="width: 35px; color: rgba(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">@@ -141,7 +187,6 @@ class PathwayMethod(base.AnalysisMethod):</td>
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141
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">index</span></span>
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142
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> </span>
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143
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># based on GSEA paper (Subramanian et al, 2005, PNAS)</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># xxx assume that Bindex is a dictionary that maps all genes into ranks, and Bscores maps all genes to SLPV</span></span>
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145
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ranks and scores are hashes from genes into ranks and SLPV</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># when p=0, ES(S) reduces to the standard K-S statistic; p=1 is used in PNAS paper</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -183,7 +228,8 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">terms2orfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">associations</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">allgenes</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;">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;">data</span><span class="p">]</span></span>
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# method=GSEA, using SLPV to rank genes, Nperm=%d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">N</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# method=GSEA, Nperm=%d, p=%d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">Nperm</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# ranking genes by %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ranking</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# total genes: %s, mean rank: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span><span class="n" style="color: #333;">n2</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># rank by SLPV=sign(LFC)*log10(pval)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,14 +241,21 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">orf</span><span class="p">,</span><span class="n" style="color: #333;">LFC</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;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</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="n" style="color: #333;">LFC_col</span><span class="p">]),</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="n" style="color: #333;">Pval_col</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">SLPV</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">LFC</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">Pval</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.000001</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="LC198" class="line" lang="python"> <span class="n" style="color: #333;">pairs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">orf</span><span class="p">,</span><span class="n" style="color: #333;">SLPV</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ranking</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"SLPV"</span><span class="p">:</span> <span class="n" style="color: #333;">pairs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">orf</span><span class="p">,</span><span class="n" style="color: #333;">SLPV</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ranking</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"LFC"</span><span class="p">:</span> <span class="n" style="color: #333;">pairs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">orf</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="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pre-randomize ORFs, to avoid genome-position bias in case of ties in pvals (e.g. 1.0)</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">indexes</span> <span class="o" style="font-weight: 600;">=</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;">pairs</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;">indexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">permutation</span><span class="p">(</span><span class="n" style="color: #333;">indexes</span><span class="p">).</span><span class="n" style="color: #333;">tolist</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;">pairs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">pairs</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;">indexes</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">pairs</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</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 class="c1" style="color: #998; font-style: italic;"># emulate ranking genes with *higher* correlation at top</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">orfs2rank</span><span class="p">,</span><span class="n" style="color: #333;">orfs2score</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},{}</span></span>
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<pre style="margin: 0;"> <span id="LC254" 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;">orf</span><span class="p">,</span><span class="n" style="color: #333;">score</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;">pairs</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;">orfs2score</span><span class="p">[</span><span class="n" style="color: #333;">orf</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">orfs2rank</span><span class="p">[</span><span class="n" style="color: #333;">orf</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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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">Nperm</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">N</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">Nperm</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">N<span class="idiff left right">perm</span></span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">,</span><span class="n" style="color: #333;">Total</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">terms</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC260" 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;">term</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;">terms</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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="307" style="width: 35px; color: rgba(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">@@ -254,38 +307,7 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</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="p">.</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="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC257" 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="LC258" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_resampling_file</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="LC260" class="line" lang="python"> <span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">hits</span><span class="p">,</span><span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[],[]</span></span>
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<pre style="margin: 0;">-<span id="LC261" 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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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span><span class="p">:</span> <span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</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="LC263" 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="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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="LC264" class="line" lang="python"> <span class="n" style="color: #333;">genes</span><span class="p">.</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>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">qval</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;">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>
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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;">qval</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;">hits</span><span class="p">.</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="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">hits</span><span class="p">,</span><span class="n" style="color: #333;">headers</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assume these are listed as pairs (tab-sep)</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return bidirectional hash (genes->[terms], terms->[genes]; each can be one-to-many, hence lists)</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_associations</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="LC272" class="line" lang="python"> <span class="n" style="color: #333;">associations</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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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;">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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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</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;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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="LC276" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># store mappings in both directions</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</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="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">w</span><span class="p">[</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;">1</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="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</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;">associations</span><span class="p">:</span> <span class="n" style="color: #333;">associations</span><span class="p">[</span><span class="n" style="color: #333;">a</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="LC279" class="line" lang="python"> <span class="n" style="color: #333;">associations</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">].</span><span class="n" style="color: #333;">append</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="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">associations</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_pathways</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="LC283" class="line" lang="python"> <span class="n" style="color: #333;">pathways</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC284" 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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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'#'</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC286" 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="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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="LC287" class="line" lang="python"> <span class="n" style="color: #333;">pathways</span><span class="p">[</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</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>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pathways</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">########## Fisher Exact Test ###############</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># HYPERGEOMETRIC </span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># scipy.stats.hypergeom.sf() is survival function (1-cdf), so only enriched genes will be significant</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -297,8 +319,6 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hypergeometric</span><span class="p">(</span><span class="bp" style="color: #999;">self</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>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hypergeom</span><span class="p">.</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>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">msg</span><span class="p">):</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fisher_exact_test</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="LC323" class="line" lang="python"> <span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">hits</span><span class="p">,</span><span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">read_resampling_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resamplingFile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">associations</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">read_associations</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">associationsFile</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -313,7 +333,7 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC333" 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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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">orf</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>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">orf</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">associations</span><span class="p">:</span> <span class="n" style="color: #333;">genes_with_associations</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="LC316" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# method=F<span class="idiff left right">ISHER</span>, PC=%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">PC</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# method=F<span class="idiff left right">ET</span>, PC=%s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">PC</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# genes with associations=%s out of %s total"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">genes_with_associations</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# significant genes (qval<0.05): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">hits</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -366,6 +386,142 @@ class PathwayMethod(base.AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Finished Pathway Enrichment Method"</span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">########## Ontologizer ###############</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this method is restricted to GO terms</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this implements the union method of:</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Grossman et al (2007). Improved Detection of overrepresentation of Gene-Ontology </span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># annotation with parent-child analysis. Bioinformatics, 23(22):3024-3031.</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">Ontologizer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">warning</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">):</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</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="n" style="color: #333;">s</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># use self.warning? prepend method name?</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> </span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># returns True if ch is a descendant of GO (as GO terms, like "GO:0006810")</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> </span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">descendant_of</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">,</span><span class="n" style="color: #333;">GO</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ch</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">GO</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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405
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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;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parents</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">ch</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">descendant_of</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">,</span><span class="n" style="color: #333;">GO</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="bp" style="color: #999;">True</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> </span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># visited is a hash</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assume B is above A</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># do upward DFS following parent pointers till hit NULL</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return all nodes on all paths? include A and B?</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> </span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_ancestors</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span><span class="n" style="color: #333;">visited</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">A</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">visited</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">visited</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">visited</span><span class="p">[</span><span class="n" style="color: #333;">A</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">parent</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parents</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,[]):</span> <span class="n" style="color: #333;">get_ancestors</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">,</span><span class="n" style="color: #333;">visited</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">visited</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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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">depth</span><span class="p">(</span><span class="n" style="color: #333;">go</span><span class="p">):</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">go</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;">parents</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">min</span><span class="p">([</span><span class="n" style="color: #333;">depth</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;">parents</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">]])</span></span>
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423
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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;">ontology</span><span class="p">,</span><span class="n" style="color: #333;">parents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},{}</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">GOannot</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">associationsFile</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">OBOfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pathwaysFile</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"></span>
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429
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<pre style="margin: 0;">+<span id="LC429" 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;">OBOfile</span><span class="p">):</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"id:"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">4</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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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[:</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"is_a:"</span><span class="p">:</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">id</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;">parents</span><span class="p">:</span> <span class="n" style="color: #333;">parents</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</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="LC434" class="line" lang="python"> <span class="n" style="color: #333;">parents</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC435" 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;">line</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[:</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"name:"</span><span class="p">:</span> <span class="n" style="color: #333;">ontology</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">6</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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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">rv2gos</span><span class="p">,</span><span class="n" style="color: #333;">go2rvs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},{}</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">MINTERMS</span><span class="p">,</span><span class="n" style="color: #333;">MAXTERMS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">300</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> </span>
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441
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<pre style="margin: 0;">+<span id="LC441" 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;">GOannot</span><span class="p">):</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" 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="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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="LC443" class="line" lang="python"> <span class="n" style="color: #333;">rv</span><span class="p">,</span><span class="n" style="color: #333;">go</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" 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;">rv2gos</span><span class="p">:</span> <span class="n" style="color: #333;">rv2gos</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>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">go</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;">rv2gos</span><span class="p">[</span><span class="n" style="color: #333;">rv</span><span class="p">]:</span> <span class="n" style="color: #333;">rv2gos</span><span class="p">[</span><span class="n" style="color: #333;">rv</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">go</span><span class="p">)</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">go</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;">go2rvs</span><span class="p">:</span> <span class="n" style="color: #333;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" 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;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">]:</span> <span class="n" style="color: #333;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">].</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="LC448" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># expand to all parents...</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">BP</span><span class="p">,</span><span class="n" style="color: #333;">CC</span><span class="p">,</span><span class="n" style="color: #333;">MF</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"GO:0008150"</span><span class="p">,</span><span class="s" style="color: #d14;">"GO:0005575"</span><span class="p">,</span><span class="s" style="color: #d14;">"GO:0003674"</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;">for</span> <span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">get_ancestors</span><span class="p">(</span><span class="n" style="color: #333;">go</span><span class="p">,{}):</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g</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;">rv2gos</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="LC452" class="line" lang="python"> <span class="n" style="color: #333;">rv2gos</span><span class="p">[</span><span class="n" style="color: #333;">rv</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g</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;">go2rvs</span><span class="p">:</span> <span class="n" style="color: #333;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">g</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="LC454" class="line" lang="python"> <span class="n" style="color: #333;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">g</span><span class="p">].</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="LC455" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"GO terms with at least one ORF: %s"</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;">go2rvs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()))</span> <span class="c1" style="color: #998; font-style: italic;"># what about between MIN and MAX?</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">go</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">go2rvs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">go</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;">ontology</span><span class="p">:</span> <span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"not found: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">go</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># also indicate which gene?</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># could use class method, but would have to adapt it: </span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># genes,hits,headers = self.read_resampling_file(self.resamplingFile)</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">genes</span><span class="p">,</span><span class="n" style="color: #333;">pvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},[]</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"> <span class="n" style="color: #333;">allorfs</span><span class="p">,</span><span class="n" style="color: #333;">studyset</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],[]</span></span>
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<pre style="margin: 0;">+<span id="LC465" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resamplingFile</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"#"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC467" 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="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">allorfs</span><span class="p">.</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="LC470" class="line" lang="python"> <span class="n" style="color: #333;">pval</span><span class="p">,</span><span class="n" style="color: #333;">qval</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;">w</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span><span class="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>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qval</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;">studyset</span><span class="p">.</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="LC472" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span><span class="p">.</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 class="n" style="color: #333;">pval</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">ranks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC475" 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="p">,</span><span class="n" style="color: #333;">pval</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;">pvals</span><span class="p">):</span> <span class="n" style="color: #333;">ranks</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;">i</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="LC476" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# number of resampling hits (qval<0.05): %s"</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;">studyset</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC478" 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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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">a</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;">allorfs</span><span class="p">),</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">studyset</span><span class="p">)</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">go</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">go2rvs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">go</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;">ontology</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">m</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;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># orfs in the GO terms in the genome overall</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">MINTERMS</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">MAXTERMS</span><span class="p">:</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">],</span><span class="n" style="color: #333;">studyset</span><span class="p">)))</span> <span class="c1" style="color: #998; font-style: italic;"># orfs with GO term in studyset</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># calc p=len(rvs for parents of go), q=len(subset of parent rvs in studyset)</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">go</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;">parents</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">npar</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;">parents</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">])</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">par</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parents</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">]:</span> <span class="n" style="color: #333;">P</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;">union</span><span class="p">(</span><span class="n" style="color: #333;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">par</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC491" 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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">),</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">intersection</span><span class="p">(</span><span class="n" style="color: #333;">studyset</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">enrich</span> <span class="o" style="font-weight: 600;">=</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 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;">q</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="p">((</span><span class="n" style="color: #333;">m</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="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># enrichment</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parents: p overall, q in studyset; GO in studyset: b out of q (subset of studyset labeled with a parent GO term)</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assume m orfs have GO term inside parent (same as overall) </span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># subtract 1 from b possibly because we are using 1-cdf? this is needed to get same numeric results as 'phypergeometric' in Ontologizer</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">hypergeom</span><span class="p">.</span><span class="n" style="color: #333;">cdf</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 class="n" style="color: #333;">p</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="n" style="color: #333;">q</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">go</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</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="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">npar</span><span class="p">,</span><span class="n" style="color: #333;">enrich</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="LC498" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC500" 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;">multitest</span><span class="p">.</span><span class="n" style="color: #333;">fdrcorrection</span><span class="p">(</span><span class="n" style="color: #333;">pvals</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC502" 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="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="p">[</span><span class="n" style="color: #333;">y</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">,</span><span class="n" style="color: #333;">qvals</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="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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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# number of GO terms that are significantly enriched (qval<0.05): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="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;">counts</span><span class="p">))))</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 1-sided pvals, only report enriched terms, not depleted</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"GO_term description total_orfs orfs_in_GO orfs_in_parents hits_in_parents hits GO_in_hits num_parent_nodes enrichment pval qval genes_in_intersection_of_hits_and_GO_term"</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()))</span> <span class="c1" style="color: #998; font-style: italic;"># assume self.outputFile has already been opened</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">go</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</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="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">npar</span><span class="p">,</span><span class="n" style="color: #333;">enrich</span><span class="p">,</span><span class="n" style="color: #333;">pval</span><span class="p">,</span><span class="n" style="color: #333;">qval</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">go2rvs</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">],</span><span class="n" style="color: #333;">studyset</span><span class="p">)</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="n" style="color: #333;">hits</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="n" style="color: #333;">genes</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="n" style="color: #333;">ranks</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;">hits</span><span class="p">]</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">hits</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># sort on ranks</span></span>
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<td class="diff-line-num new new_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"%s/%s(%s)"</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="n" style="color: #333;">rank</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</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;">rank</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hits</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">hits</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># add gene names</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" 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;">go</span><span class="p">,</span><span class="n" style="color: #333;">ontology</span><span class="p">[</span><span class="n" style="color: #333;">go</span><span class="p">],</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">m</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="p">,</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="n" style="color: #333;">npar</span><span class="p">,</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">enrich</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="p">),</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">pval</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">),</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">qval</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">),</span><span class="n" style="color: #333;">hits</span><span class="p">]</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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="p">.</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>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Adding File: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">outputFile</span><span class="p">))</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">add_file</span><span class="p">(</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Pathway Enrichment"</span><span class="p">)</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">()</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Finished Pathway Enrichment Method"</span><span class="p">)</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>
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369
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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;">####################################################</span></span>
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370
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="python"></span>
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371
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<pre style="margin: 0;"> <span id="LC527" 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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<li id="b1616bd66829b174aefbf8f12356d430430acbad">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#b1616bd66829b174aefbf8f12356d430430acbad"><strong>src/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt</strong></a>
The diff for this file was not included because it is too large.
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<li id="0517df3fd9965095cce6712ccae8ceb6727b7be8">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#0517df3fd9965095cce6712ccae8ceb6727b7be8"><strong>src/pytransit/data/H37Rv_COG_roles.dat</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">@@ -40,7 +40,6 @@ Rv0054 L ssb Replication, recombination and repair</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Rv0055 J rpsR Translation, ribosomal structure and biogenesis </span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Rv0056 J rplI Translation, ribosomal structure and biogenesis </span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Rv0058 L dnaB Replication, recombination and repair </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">Rv0058 L dnaB Replication, recombination and repair </span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Rv0060 R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Rv0062 G celA1 Carbohydrate transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Rv0063 C - Energy production and conversion </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +65,6 @@ Rv0084 C hycD Energy production and conversion</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">Rv0085 C hycP Energy production and conversion </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">Rv0086 P hycQ Inorganic ion transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">Rv0087 C hycE Energy production and conversion </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">Rv0087 C hycE Energy production and conversion </span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">Rv0088 J - Translation, ribosomal structure and biogenesis </span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">Rv0089 R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">Rv0090 P - Inorganic ion transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,7 +76,6 @@ Rv0097 Q - Secondary metabolites biosynthesis, transport and catabolism</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">Rv0099 Q fadD10 Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">Rv0100 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">Rv0101 Q nrp Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">Rv0101 Q nrp Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">Rv0102 S - Function unknown </span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">Rv0103c P ctpB Inorganic ion transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">Rv0104 T - Signal transduction mechanisms </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,11 +132,11 @@ Rv0165c K - Transcription</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext">Rv0166 Q fadD5 Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">Rv0167 Q yrbE1A Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">Rv0168 Q yrbE1B Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">Rv0169 T mce1A Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext">Rv0169 Q mce1A Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">Rv0169 T mce1A Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext">Rv0170 Q mce1B Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext">Rv0171 T mce1C Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">Rv0171 Q mce1C Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">Rv0171 T mce1C Signal transduction mechanisms </span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">Rv0172 Q mce1D Secondary metabolites biosynthesis, transport and catabolism </span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext">Rv0173 Q lprK Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext">Rv0174 Q mce1F Secondary metabolites biosynthesis, transport and catabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,7 +165,6 @@ Rv0207c S - Function unknown</td>
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168
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext">Rv0208c R trmB General function prediction only </span>
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169
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext">Rv0211 C pckA Energy production and conversion </span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">Rv0212c H nadR Coenzyme transport and metabolism </span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext">Rv0212c H nadR Coenzyme transport and metabolism </span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">Rv0213c C - Energy production and conversion </span>
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173
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">Rv0214 Q fadD4 Secondary metabolites biosynthesis, transport and catabolism </span>
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174
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext">Rv0215c I fadE3 Lipid transport and metabolism </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" style="width: 35px; color: rgba(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">@@ -204,15 +200,14 @@ Rv0253 R nirD General function prediction only</td>
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204
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext">Rv0254c H cobU Coenzyme transport and metabolism </span>
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205
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext">Rv0255c H cobQ1 Coenzyme transport and metabolism </span>
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206
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext">Rv0259c S - Function unknown </span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">Rv0260c K - Transcription </span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="plaintext">Rv0260c H - Coenzyme transport and metabolism </span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">Rv0260c K - Transcription </span>
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209
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext">Rv0261c P narK3 Inorganic ion transport and metabolism </span>
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210
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext">Rv0262c R aac General function prediction only </span>
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211
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext">Rv0263c E - Amino acid transport and metabolism </span>
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212
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext">Rv0264c E - Amino acid transport and metabolism </span>
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213
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext">Rv0265c P - Inorganic ion transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext">Rv0266c Q oplA Secondary metabolites biosynthesis, transport and catabolism </span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext">Rv0266c Q oplA Secondary metabolites biosynthesis, transport and catabolism </span>
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">Rv0267 P narU Inorganic ion transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext">Rv0268c D - Cell cycle control, cell division, chromosome partitioning </span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">Rv0269c L - Replication, recombination and repair </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -248,8 +243,8 @@ Rv0319 O pcp Posttranslational modification, protein turnover, chaperones</td>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="plaintext">Rv0321 F dcd Nucleotide transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext">Rv0322 M udgA Cell wall/membrane/envelope biogenesis </span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext">Rv0323c S - Function unknown </span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="plaintext">Rv0324 P - Inorganic ion transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext">Rv0324 K - Transcription </span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">Rv0324 P - Inorganic ion transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext">Rv0325 R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext">Rv0326 R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext">Rv0327c Q cyp135A1 Secondary metabolites biosynthesis, transport and catabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -261,7 +256,6 @@ Rv0334 M rmlA Cell wall/membrane/envelope biogenesis</td>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">Rv0337c E aspC Amino acid transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext">Rv0338c C - Energy production and conversion </span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext">Rv0339c K - Transcription </span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext">Rv0339c K - Transcription </span>
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext">Rv0342 R iniA General function prediction only </span>
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext">Rv0343 R iniC General function prediction only </span>
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267
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext">Rv0345 R - General function prediction only </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -295,10 +289,9 @@ Rv0380c J - Translation, ribosomal structure and biogenesis</td>
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295
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="plaintext">Rv0382c F pyrE Nucleotide transport and metabolism </span>
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296
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="plaintext">Rv0384c O clpB Posttranslational modification, protein turnover, chaperones </span>
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297
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="plaintext">Rv0385 C - Energy production and conversion </span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="plaintext">Rv0385 C - Energy production and conversion </span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="plaintext">Rv0386 T - Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="plaintext">Rv0386 K - Transcription </span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="plaintext">Rv0386 R - General function prediction only </span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">Rv0386 T - Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="plaintext">Rv0389 F purT Nucleotide transport and metabolism </span>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="plaintext">Rv0390 P - Inorganic ion transport and metabolism </span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="plaintext">Rv0391 E metZ Amino acid transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -347,8 +340,8 @@ Rv0449c R - General function prediction only</td>
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347
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="plaintext">Rv0450c R mmpL4 General function prediction only </span>
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348
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="plaintext">Rv0452 K - Transcription </span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="plaintext">Rv0454 J - Translation, ribosomal structure and biogenesis </span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="plaintext">Rv0456c I echA2 Lipid transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="plaintext">Rv0456A T - Signal transduction mechanisms </span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">Rv0456c I echA2 Lipid transport and metabolism </span>
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="plaintext">Rv0457c E - Amino acid transport and metabolism </span>
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="plaintext">Rv0458 C - Energy production and conversion </span>
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354
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="plaintext">Rv0459 S - Function unknown </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -360,8 +353,8 @@ Rv0466 I - Lipid transport and metabolism</td>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="plaintext">Rv0467 C icl Energy production and conversion </span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext">Rv0468 I fadB2 Lipid transport and metabolism </span>
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext">Rv0469 M umaA Cell wall/membrane/envelope biogenesis </span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="plaintext">Rv0470c M pcaA Cell wall/membrane/envelope biogenesis </span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext">Rv0470A H - Coenzyme transport and metabolism </span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">Rv0470c M pcaA Cell wall/membrane/envelope biogenesis </span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext">Rv0472c K - Transcription </span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="plaintext">Rv0473 S - Function unknown </span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="plaintext">Rv0474 K - Transcription </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -392,7 +385,6 @@ Rv0508 C - Energy production and conversion</td>
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392
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="plaintext">Rv0509 H hemA Coenzyme transport and metabolism </span>
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="plaintext">Rv0510 H hemC Coenzyme transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="plaintext">Rv0511 H hemD Coenzyme transport and metabolism </span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="plaintext">Rv0511 H hemD Coenzyme transport and metabolism </span>
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="plaintext">Rv0512 H hemB Coenzyme transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="plaintext">Rv0516c T - Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="plaintext">Rv0517 I - Lipid transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -437,9 +429,8 @@ Rv0566c S - Function unknown</td>
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="plaintext">Rv0567 R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="plaintext">Rv0568 Q cyp135B1 Secondary metabolites biosynthesis, transport and catabolism </span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="plaintext">Rv0570 F nrdZ Nucleotide transport and metabolism </span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="plaintext">Rv0571c R - General function prediction only </span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="plaintext">Rv0571c R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="plaintext">Rv0571c I - Lipid transport and metabolism </span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext">Rv0571c R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="plaintext">Rv0573c H - Coenzyme transport and metabolism </span>
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="plaintext">Rv0574c M - Cell wall/membrane/envelope biogenesis </span>
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="plaintext">Rv0575c C - Energy production and conversion </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -485,11 +476,10 @@ Rv0627 R - General function prediction only</td>
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="plaintext">Rv0628c S - Function unknown </span>
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486
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477
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="plaintext">Rv0629c L recD Replication, recombination and repair </span>
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="plaintext">Rv0630c L recB Replication, recombination and repair </span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="plaintext">Rv0630c L recB Replication, recombination and repair </span>
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489
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479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="plaintext">Rv0631c L recC Replication, recombination and repair </span>
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490
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480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="plaintext">Rv0632c I echA3 Lipid transport and metabolism </span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="plaintext">Rv0634c R - General function prediction only </span>
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492
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="plaintext">Rv0634B J rpmG Translation, ribosomal structure and biogenesis </span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">Rv0634c R - General function prediction only </span>
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="plaintext">Rv0636 I - Lipid transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="plaintext">Rv0638 U secE Intracellular trafficking, secretion, and vesicular transport </span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="plaintext">Rv0639 K nusG Transcription </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -663,7 +653,6 @@ Rv0855 C far Energy production and conversion</td>
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663
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653
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="plaintext">Rv0858c E - Amino acid transport and metabolism </span>
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="plaintext">Rv0859 I fadA Lipid transport and metabolism </span>
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="plaintext">Rv0860 I fadB Lipid transport and metabolism </span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="plaintext">Rv0860 I fadB Lipid transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="plaintext">Rv0861c L ercc3 Replication, recombination and repair </span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="plaintext">Rv0864 H moaC Coenzyme transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="plaintext">Rv0865 H mog Coenzyme transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -678,8 +667,8 @@ Rv0876c R - General function prediction only</td>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="plaintext">Rv0880 K - Transcription </span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="plaintext">Rv0881 J - Translation, ribosomal structure and biogenesis </span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="plaintext">Rv0884c E serC Amino acid transport and metabolism </span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="plaintext">Rv0886 R fprB General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="plaintext">Rv0886 C fprB Energy production and conversion </span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext">Rv0886 R fprB General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="plaintext">Rv0887c S - Function unknown </span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="plaintext">Rv0889c C citA Energy production and conversion </span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="plaintext">Rv0890c K - Transcription </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -695,7 +684,6 @@ Rv0899 M ompA Cell wall/membrane/envelope biogenesis</td>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="plaintext">Rv0902c T prrB Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="plaintext">Rv0903c K prrA Transcription </span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="plaintext">Rv0904c I accD3 Lipid transport and metabolism </span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="plaintext">Rv0904c I accD3 Lipid transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="plaintext">Rv0905 I echA6 Lipid transport and metabolism </span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="plaintext">Rv0906 R - General function prediction only </span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="plaintext">Rv0907 V - Defense mechanisms </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -709,8 +697,8 @@ Rv0919 R - General function prediction only</td>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="plaintext">Rv0920c L - Replication, recombination and repair </span>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="plaintext">Rv0921 L - Replication, recombination and repair </span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="plaintext">Rv0922 L - Replication, recombination and repair </span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="plaintext">Rv0923c S - Function unknown </span>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="plaintext">Rv0923c R - General function prediction only </span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="plaintext">Rv0923c S - Function unknown </span>
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="plaintext">Rv0924c P mntH Inorganic ion transport and metabolism </span>
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="plaintext">Rv0925c R - General function prediction only </span>
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716
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="plaintext">Rv0926c S - Function unknown </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -727,7 +715,6 @@ Rv0935 P pstC1 Inorganic ion transport and metabolism</td>
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727
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="plaintext">Rv0936 P pstA2 Inorganic ion transport and metabolism </span>
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728
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="plaintext">Rv0937c S - Function unknown </span>
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729
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="plaintext">Rv0938 L - Replication, recombination and repair </span>
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730
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="plaintext">Rv0938 L - Replication, recombination and repair </span>
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731
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="plaintext">Rv0939 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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732
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="plaintext">Rv0939 R - General function prediction only </span>
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733
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="plaintext">Rv0940c C - Energy production and conversion </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -753,8 +740,6 @@ Rv0969 P ctpV Inorganic ion transport and metabolism</td>
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753
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="plaintext">Rv0971c I echA7 Lipid transport and metabolism </span>
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754
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="plaintext">Rv0972c I fadE12 Lipid transport and metabolism </span>
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755
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="plaintext">Rv0973c I accA2 Lipid transport and metabolism </span>
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756
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="plaintext">Rv0973c I accA2 Lipid transport and metabolism </span>
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757
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="plaintext">Rv0973c I accA2 Lipid transport and metabolism </span>
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758
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743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="plaintext">Rv0974c I accD2 Lipid transport and metabolism </span>
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759
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744
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="plaintext">Rv0975c I fadE13 Lipid transport and metabolism </span>
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760
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745
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="plaintext">Rv0978c S PE_PGRS17 Function unknown </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -897,8 +882,8 @@ Rv1166 E lpqW Amino acid transport and metabolism</td>
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897
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="plaintext">Rv1167c K - Transcription </span>
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898
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="plaintext">Rv1170 S mshB Function unknown </span>
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899
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="plaintext">Rv1173 R fbiC General function prediction only </span>
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900
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="plaintext">Rv1175c R fadH General function prediction only </span>
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901
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="plaintext">Rv1175c C fadH Energy production and conversion </span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="plaintext">Rv1175c R fadH General function prediction only </span>
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902
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="plaintext">Rv1176c K - Transcription </span>
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="plaintext">Rv1177 C fdxC Energy production and conversion </span>
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="plaintext">Rv1178 E - Amino acid transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -957,7 +942,6 @@ Rv1245c R - General function prediction only</td>
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="plaintext">Rv1246c D - Cell cycle control, cell division, chromosome partitioning </span>
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958
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="plaintext">Rv1247c D - Cell cycle control, cell division, chromosome partitioning </span>
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959
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944
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="plaintext">Rv1248c C kgd Energy production and conversion </span>
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960
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="plaintext">Rv1248c C kgd Energy production and conversion </span>
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961
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945
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<pre style="margin: 0;"> <span id="LC945" class="line" lang="plaintext">Rv1250 R - General function prediction only </span>
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962
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946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="plaintext">Rv1251c L - Replication, recombination and repair </span>
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963
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="plaintext">Rv1251c R - General function prediction only </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -974,7 +958,6 @@ Rv1263 J amiB2 Translation, ribosomal structure and biogenesis</td>
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974
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="plaintext">Rv1264 T - Signal transduction mechanisms </span>
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="plaintext">Rv1266c L pknH Replication, recombination and repair </span>
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="plaintext">Rv1267c T embR Signal transduction mechanisms </span>
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<pre style="margin: 0;">-<span id="LC977" class="line" lang="plaintext">Rv1267c T embR Signal transduction mechanisms </span>
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="plaintext">Rv1272c V - Defense mechanisms </span>
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979
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962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="plaintext">Rv1273c V - Defense mechanisms </span>
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="plaintext">Rv1276c T - Signal transduction mechanisms </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -989,10 +972,9 @@ Rv1283c P oppB Inorganic ion transport and metabolism</td>
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989
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972
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="plaintext">Rv1284 P - Inorganic ion transport and metabolism </span>
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990
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="plaintext">Rv1285 H cysD Coenzyme transport and metabolism </span>
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991
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="plaintext">Rv1286 P cysN Inorganic ion transport and metabolism </span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="plaintext">Rv1286 P cysN Inorganic ion transport and metabolism </span>
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="plaintext">Rv1287 K - Transcription </span>
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="plaintext">Rv1288 R - General function prediction only </span>
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995
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="plaintext">Rv1288 M - Cell wall/membrane/envelope biogenesis </span>
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="plaintext">Rv1288 R - General function prediction only </span>
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978
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<pre style="margin: 0;"> <span id="LC978" class="line" lang="plaintext">Rv1290c S - Function unknown </span>
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979
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<pre style="margin: 0;"> <span id="LC979" class="line" lang="plaintext">Rv1292 J argS Translation, ribosomal structure and biogenesis </span>
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998
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980
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<pre style="margin: 0;"> <span id="LC980" class="line" lang="plaintext">Rv1293 E lysA Amino acid transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1009,7 +991,6 @@ Rv1304 C atpB Energy production and conversion</td>
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1009
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991
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="plaintext">Rv1305 C atpE Energy production and conversion </span>
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1010
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="plaintext">Rv1306 C atpF Energy production and conversion </span>
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1011
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993
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="plaintext">Rv1307 C atpH Energy production and conversion </span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="plaintext">Rv1307 C atpH Energy production and conversion </span>
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1013
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994
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="plaintext">Rv1308 C atpA Energy production and conversion </span>
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1014
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995
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<pre style="margin: 0;"> <span id="LC995" class="line" lang="plaintext">Rv1309 C atpG Energy production and conversion </span>
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1015
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996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="plaintext">Rv1310 C atpD Energy production and conversion </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1018,8 +999,8 @@ Rv1313c L - Replication, recombination and repair</td>
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1018
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999
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="plaintext">Rv1314c S - Function unknown </span>
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1019
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1000
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="plaintext">Rv1315 M murA Cell wall/membrane/envelope biogenesis </span>
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1020
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="plaintext">Rv1316c L ogt Replication, recombination and repair </span>
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1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="plaintext">Rv1317c L alkA Replication, recombination and repair </span>
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1022
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1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="plaintext">Rv1317c F alkA Nucleotide transport and metabolism </span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="plaintext">Rv1317c L alkA Replication, recombination and repair </span>
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1023
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1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="plaintext">Rv1318c T - Signal transduction mechanisms </span>
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1024
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="plaintext">Rv1319c T - Signal transduction mechanisms </span>
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1025
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1006
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="plaintext">Rv1320c T - Signal transduction mechanisms </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1047,23 +1028,21 @@ Rv1344 Q - Secondary metabolites biosynthesis, transport and catabolism</td>
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1047
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="plaintext">Rv1345 Q fadD33 Secondary metabolites biosynthesis, transport and catabolism </span>
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1048
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="plaintext">Rv1346 I fadE14 Lipid transport and metabolism </span>
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1049
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1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="plaintext">Rv1347c J - Translation, ribosomal structure and biogenesis </span>
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1050
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="plaintext">Rv1348 V - Defense mechanisms </span>
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1051
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1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="plaintext">Rv1348 P - Inorganic ion transport and metabolism </span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="plaintext">Rv1348 V - Defense mechanisms </span>
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1052
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1033
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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="plaintext">Rv1349 V - Defense mechanisms </span>
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1053
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1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="plaintext">Rv1350 R fabG General function prediction only </span>
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1054
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1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="plaintext">Rv1353c K - Transcription </span>
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1055
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="plaintext">Rv1354c T - Signal transduction mechanisms </span>
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1056
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<pre style="margin: 0;">-<span id="LC1056" class="line" lang="plaintext">Rv1354c T - Signal transduction mechanisms </span>
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1057
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="plaintext">Rv1355c H moeY Coenzyme transport and metabolism </span>
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1058
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="plaintext">Rv1357c T - Signal transduction mechanisms </span>
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1059
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<pre style="margin: 0;">-<span id="LC1059" class="line" lang="plaintext">Rv1358 T - Signal transduction mechanisms </span>
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1060
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="plaintext">Rv1358 K - Transcription </span>
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1061
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="plaintext">Rv1358 R - General function prediction only </span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="plaintext">Rv1358 T - Signal transduction mechanisms </span>
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1062
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="plaintext">Rv1359 T - Signal transduction mechanisms </span>
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1063
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="plaintext">Rv1360 C - Energy production and conversion </span>
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1064
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<pre style="margin: 0;">-<span id="LC1064" class="line" lang="plaintext">Rv1364c T - Signal transduction mechanisms </span>
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1065
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<pre style="margin: 0;">-<span id="LC1065" class="line" lang="plaintext">Rv1364c T - Signal transduction mechanisms </span>
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1066
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1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="plaintext">Rv1364c K - Transcription </span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="plaintext">Rv1364c T - Signal transduction mechanisms </span>
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1067
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="plaintext">Rv1365c T rsfA Signal transduction mechanisms </span>
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1068
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1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="plaintext">Rv1366 S - Function unknown </span>
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1069
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1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="plaintext">Rv1367c V - Defense mechanisms </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1099,13 +1078,11 @@ Rv1406 J fmt Translation, ribosomal structure and biogenesis</td>
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1099
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1078
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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="plaintext">Rv1407 J fmu Translation, ribosomal structure and biogenesis </span>
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1100
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1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="plaintext">Rv1408 G rpe Carbohydrate transport and metabolism </span>
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1101
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1080
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="plaintext">Rv1409 H ribG Coenzyme transport and metabolism </span>
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1102
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="plaintext">Rv1409 H ribG Coenzyme transport and metabolism </span>
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1103
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1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="plaintext">Rv1410c R - General function prediction only </span>
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1104
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1082
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="plaintext">Rv1412 H ribC Coenzyme transport and metabolism </span>
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1105
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1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="plaintext">Rv1413 E - Amino acid transport and metabolism </span>
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1106
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="plaintext">Rv1414 E - Amino acid transport and metabolism </span>
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1107
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="plaintext">Rv1415 H ribA2 Coenzyme transport and metabolism </span>
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1108
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<pre style="margin: 0;">-<span id="LC1108" class="line" lang="plaintext">Rv1415 H ribA2 Coenzyme transport and metabolism </span>
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1109
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1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="plaintext">Rv1416 H ribH Coenzyme transport and metabolism </span>
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1110
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1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="plaintext">Rv1420 L uvrC Replication, recombination and repair </span>
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1111
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1088
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="plaintext">Rv1421 R - General function prediction only </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1136" style="width: 35px; color: rgba(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="1113" style="width: 35px; color: rgba(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">@@ -1136,8 +1113,8 @@ Rv1456c O - Posttranslational modification, protein turnover, chaperones</td>
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1136
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="plaintext">Rv1457c V - Defense mechanisms </span>
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1137
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1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="plaintext">Rv1458c V - Defense mechanisms </span>
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1138
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="plaintext">Rv1460 K - Transcription </span>
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1139
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="plaintext">Rv1461 O - Posttranslational modification, protein turnover, chaperones </span>
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1140
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="plaintext">Rv1461 L - Replication, recombination and repair </span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="plaintext">Rv1461 O - Posttranslational modification, protein turnover, chaperones </span>
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1141
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1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="plaintext">Rv1462 O - Posttranslational modification, protein turnover, chaperones </span>
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1142
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1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="plaintext">Rv1463 O - Posttranslational modification, protein turnover, chaperones </span>
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1143
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="plaintext">Rv1464 E csd Amino acid transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1164,14 +1141,12 @@ Rv1488 O - Posttranslational modification, protein turnover, chaperones</td>
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1164
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="plaintext">Rv1489A I - Lipid transport and metabolism </span>
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1165
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="plaintext">Rv1491c S - Function unknown </span>
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1166
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="plaintext">Rv1492 I mutA Lipid transport and metabolism </span>
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1167
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<pre style="margin: 0;">-<span id="LC1167" class="line" lang="plaintext">Rv1492 I mutA Lipid transport and metabolism </span>
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1168
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<pre style="margin: 0;">-<span id="LC1168" class="line" lang="plaintext">Rv1493 I mutB Lipid transport and metabolism </span>
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1169
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="plaintext">Rv1493 I mutB Lipid transport and metabolism </span>
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1170
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1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="plaintext">Rv1495 T - Signal transduction mechanisms </span>
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="plaintext">Rv1496 E - Amino acid transport and metabolism </span>
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="plaintext">Rv1497 V lipL Defense mechanisms </span>
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1173
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<pre style="margin: 0;">-<span id="LC1173" class="line" lang="plaintext">Rv1498c R - General function prediction only </span>
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1174
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1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="plaintext">Rv1498A S - Function unknown </span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="plaintext">Rv1498c R - General function prediction only </span>
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1175
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="plaintext">Rv1500 M - Cell wall/membrane/envelope biogenesis </span>
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1176
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1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="plaintext">Rv1501 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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1177
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1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="plaintext">Rv1502 G - Carbohydrate transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1272,7 +1247,6 @@ Rv1626 T - Signal transduction mechanisms</td>
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1272
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1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="plaintext">Rv1627c I - Lipid transport and metabolism </span>
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1273
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1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="plaintext">Rv1628c R - General function prediction only </span>
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1274
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1249
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="plaintext">Rv1629 L polA Replication, recombination and repair </span>
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1275
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<pre style="margin: 0;">-<span id="LC1275" class="line" lang="plaintext">Rv1629 L polA Replication, recombination and repair </span>
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1276
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1250
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="plaintext">Rv1630 J rpsA Translation, ribosomal structure and biogenesis </span>
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1277
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="plaintext">Rv1631 H coaE Coenzyme transport and metabolism </span>
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1278
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1252
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="plaintext">Rv1631 S coaE Function unknown </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1315,16 +1289,16 @@ Rv1668c R - General function prediction only</td>
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1315
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="plaintext">Rv1670 S - Function unknown </span>
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1316
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1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="plaintext">Rv1672c R - General function prediction only </span>
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1317
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1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="plaintext">Rv1673c E - Amino acid transport and metabolism </span>
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1318
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<pre style="margin: 0;">-<span id="LC1318" class="line" lang="plaintext">Rv1674c P - Inorganic ion transport and metabolism </span>
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1319
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1292
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="plaintext">Rv1674c K - Transcription </span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="plaintext">Rv1674c P - Inorganic ion transport and metabolism </span>
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1320
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1294
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="plaintext">Rv1675c T - Signal transduction mechanisms </span>
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1321
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1295
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="plaintext">Rv1676 E - Amino acid transport and metabolism </span>
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1322
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1296
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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="plaintext">Rv1677 C dsbF Energy production and conversion </span>
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1323
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1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="plaintext">Rv1679 I fadE16 Lipid transport and metabolism </span>
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1324
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1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="plaintext">Rv1680 P - Inorganic ion transport and metabolism </span>
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1325
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<td class="diff-line-num new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="plaintext">Rv1681 R moeX General function prediction only </span>
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1326
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<pre style="margin: 0;">-<span id="LC1326" class="line" lang="plaintext">Rv1683 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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1327
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1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="plaintext">Rv1683 I - Lipid transport and metabolism </span>
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<td class="diff-line-num new new_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="plaintext">Rv1683 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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1328
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<td class="diff-line-num new_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="plaintext">Rv1684 S - Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1329
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<td class="diff-line-num new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="plaintext">Rv1685c K - Transcription </span>
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<td class="diff-line-num old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1330
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<td class="diff-line-num new_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="plaintext">Rv1686c V - Defense mechanisms </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1370" style="width: 35px; color: rgba(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="1344" style="width: 35px; color: rgba(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">@@ -1370,8 +1344,6 @@ Rv1732c C - Energy production and conversion</td>
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1370
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="plaintext">Rv1734c C - Energy production and conversion </span>
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<td class="diff-line-num old_line" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1371
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<td class="diff-line-num new_line" data-linenumber="1345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="plaintext">Rv1735c P - Inorganic ion transport and metabolism </span>
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1372
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<td class="diff-line-num new_line" data-linenumber="1346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="plaintext">Rv1736c C narX Energy production and conversion </span>
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1373
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<pre style="margin: 0;">-<span id="LC1373" class="line" lang="plaintext">Rv1736c C narX Energy production and conversion </span>
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1374
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<pre style="margin: 0;">-<span id="LC1374" class="line" lang="plaintext">Rv1736c C narX Energy production and conversion </span>
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1375
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="plaintext">Rv1737c P narK2 Inorganic ion transport and metabolism </span>
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1376
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<td class="diff-line-num new_line" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="plaintext">Rv1739c P - Inorganic ion transport and metabolism </span>
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1377
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1349
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<pre style="margin: 0;"> <span id="LC1349" class="line" lang="plaintext">Rv1740 S - Function unknown </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1389" style="width: 35px; color: rgba(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="1361" style="width: 35px; color: rgba(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">@@ -1389,8 +1361,8 @@ Rv1757c L - Replication, recombination and repair</td>
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1389
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1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="plaintext">Rv1762c S - Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1390
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<td class="diff-line-num new_line" data-linenumber="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="plaintext">Rv1763 L - Replication, recombination and repair </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1391
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<td class="diff-line-num new_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="plaintext">Rv1764 L - Replication, recombination and repair </span>
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<td class="diff-line-num old old_line" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1392
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<pre style="margin: 0;">-<span id="LC1392" class="line" lang="plaintext">Rv1765c K - Transcription </span>
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<td class="diff-line-num old_line" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1393
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1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="plaintext">Rv1765A L - Replication, recombination and repair </span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="plaintext">Rv1765c K - Transcription </span>
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1394
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<td class="diff-line-num new_line" data-linenumber="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1366
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<pre style="margin: 0;"> <span id="LC1366" class="line" lang="plaintext">Rv1766 S - Function unknown </span>
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1395
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1367
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<pre style="margin: 0;"> <span id="LC1367" class="line" lang="plaintext">Rv1767 S - Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="plaintext">Rv1769 E - Amino acid transport and metabolism </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1426" style="width: 35px; color: rgba(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="1398" style="width: 35px; color: rgba(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">@@ -1426,7 +1398,6 @@ Rv1828 K - Transcription</td>
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1426
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<td class="diff-line-num new_line" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1398
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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="plaintext">Rv1829 S - Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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<td class="diff-line-num new_line" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1399
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<pre style="margin: 0;"> <span id="LC1399" class="line" lang="plaintext">Rv1830 K - Transcription </span>
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<td class="diff-line-num old_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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<td class="diff-line-num new_line" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1400
</td>
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="plaintext">Rv1832 E gcvB Amino acid transport and metabolism </span>
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<td class="diff-line-num old old_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1429
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<td class="diff-line-num new_line old" data-linenumber="1401" style="width: 35px; color: rgba(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="LC1429" class="line" lang="plaintext">Rv1832 E gcvB Amino acid transport and metabolism </span>
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<td class="diff-line-num old_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1430
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<td class="diff-line-num new_line" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1401
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1401" class="line" lang="plaintext">Rv1833c R - General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1431
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<td class="diff-line-num new_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1402
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="plaintext">Rv1834 R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1432
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<td class="diff-line-num new_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1403
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="plaintext">Rv1835c R - General function prediction only </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1450" style="width: 35px; color: rgba(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="1421" style="width: 35px; color: rgba(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">@@ -1450,8 +1421,8 @@ Rv1855c C - Energy production and conversion</td>
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1450
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<td class="diff-line-num new_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="plaintext">Rv1856c R - General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1451
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<td class="diff-line-num new_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1422
</td>
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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="plaintext">Rv1857 P modA Inorganic ion transport and metabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1452
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<td class="diff-line-num new_line" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="plaintext">Rv1858 P modB Inorganic ion transport and metabolism </span>
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<td class="diff-line-num old old_line" data-linenumber="1453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1453
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<td class="diff-line-num new_line old" data-linenumber="1424" style="width: 35px; color: rgba(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="LC1453" class="line" lang="plaintext">Rv1859 P modC Inorganic ion transport and metabolism </span>
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1454
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1424
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<pre style="margin: 0;"> <span id="LC1424" class="line" lang="plaintext">Rv1859 G modC Carbohydrate transport and metabolism </span>
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<td class="diff-line-num new old_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="plaintext">Rv1859 P modC Inorganic ion transport and metabolism </span>
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1455
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<td class="diff-line-num new_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1426
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<pre style="margin: 0;"> <span id="LC1426" class="line" lang="plaintext">Rv1861 S - Function unknown </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1456
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<td class="diff-line-num new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="plaintext">Rv1862 R adhA General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1457
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<td class="diff-line-num new_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1428" class="line" lang="plaintext">Rv1863c R - General function prediction only </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1483" style="width: 35px; color: rgba(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="1454" style="width: 35px; color: rgba(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">@@ -1483,7 +1454,6 @@ Rv1899c R lppD General function prediction only</td>
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<td class="diff-line-num old_line" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1483
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1454
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<pre style="margin: 0;"> <span id="LC1454" class="line" lang="plaintext">Rv1900c R lipJ General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1484
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<td class="diff-line-num new_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1455
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<pre style="margin: 0;"> <span id="LC1455" class="line" lang="plaintext">Rv1900c T lipJ Signal transduction mechanisms </span>
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<td class="diff-line-num old_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1485
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1456
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<pre style="margin: 0;"> <span id="LC1456" class="line" lang="plaintext">Rv1901 R cinA General function prediction only </span>
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<td class="diff-line-num old old_line" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1486
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<pre style="margin: 0;">-<span id="LC1486" class="line" lang="plaintext">Rv1901 R cinA General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1487
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1457
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<pre style="margin: 0;"> <span id="LC1457" class="line" lang="plaintext">Rv1902c R nanT General function prediction only </span>
</pre>
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1488
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1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="plaintext">Rv1903 S - Function unknown </span>
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1489
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1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="plaintext">Rv1904 T - Signal transduction mechanisms </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1505" style="width: 35px; color: rgba(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="1475" style="width: 35px; color: rgba(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">@@ -1505,18 +1475,15 @@ Rv1927 S - Function unknown</td>
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1505
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1475
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="plaintext">Rv1928c R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1506
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1476
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<pre style="margin: 0;"> <span id="LC1476" class="line" lang="plaintext">Rv1930c R - General function prediction only </span>
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1507
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1477
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<pre style="margin: 0;"> <span id="LC1477" class="line" lang="plaintext">Rv1931c K - Transcription </span>
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1508
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<pre style="margin: 0;">-<span id="LC1508" class="line" lang="plaintext">Rv1931c K - Transcription </span>
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<td class="diff-line-num old_line" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1509
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1478
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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="plaintext">Rv1932 O tpx Posttranslational modification, protein turnover, chaperones </span>
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1510
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<td class="diff-line-num new_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1479
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="plaintext">Rv1933c I fadE18 Lipid transport and metabolism </span>
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1511
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1480
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<pre style="margin: 0;"> <span id="LC1480" class="line" lang="plaintext">Rv1934c I fadE17 Lipid transport and metabolism </span>
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1512
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1481
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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="plaintext">Rv1935c I echA13 Lipid transport and metabolism </span>
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<td class="diff-line-num old_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1513
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1482
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<pre style="margin: 0;"> <span id="LC1482" class="line" lang="plaintext">Rv1936 C - Energy production and conversion </span>
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1514
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1483
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<pre style="margin: 0;"> <span id="LC1483" class="line" lang="plaintext">Rv1937 C - Energy production and conversion </span>
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1515
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<pre style="margin: 0;">-<span id="LC1515" class="line" lang="plaintext">Rv1937 C - Energy production and conversion </span>
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1516
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1484
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="plaintext">Rv1938 R ephB General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
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1485
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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="plaintext">Rv1939 R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1518
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1486
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="plaintext">Rv1940 H ribA1 Coenzyme transport and metabolism </span>
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1519
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<pre style="margin: 0;">-<span id="LC1519" class="line" lang="plaintext">Rv1940 H ribA1 Coenzyme transport and metabolism </span>
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1520
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1487
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<pre style="margin: 0;"> <span id="LC1487" class="line" lang="plaintext">Rv1941 R - General function prediction only </span>
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1521
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1488
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<pre style="margin: 0;"> <span id="LC1488" class="line" lang="plaintext">Rv1942c T - Signal transduction mechanisms </span>
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1522
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1489
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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="plaintext">Rv1944c U - Intracellular trafficking, secretion, and vesicular transport </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1544" style="width: 35px; color: rgba(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="1511" style="width: 35px; color: rgba(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">@@ -1544,8 +1511,8 @@ Rv1985c K - Transcription</td>
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1544
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1511
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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="plaintext">Rv1986 R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1545
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<td class="diff-line-num new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="plaintext">Rv1988 J - Translation, ribosomal structure and biogenesis </span>
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<td class="diff-line-num old_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1546
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1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="plaintext">Rv1989c S - Function unknown </span>
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1547
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<pre style="margin: 0;">-<span id="LC1547" class="line" lang="plaintext">Rv1990c K - Transcription </span>
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1548
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<td class="diff-line-num new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="plaintext">Rv1990A R - General function prediction only </span>
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<td class="diff-line-num new old_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="plaintext">Rv1990c K - Transcription </span>
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1549
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1516
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="plaintext">Rv1991c T - Signal transduction mechanisms </span>
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1550
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<td class="diff-line-num new_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="plaintext">Rv1992c P ctpG Inorganic ion transport and metabolism </span>
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1551
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<td class="diff-line-num new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1518
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<pre style="margin: 0;"> <span id="LC1518" class="line" lang="plaintext">Rv1994c K - Transcription </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1554" style="width: 35px; color: rgba(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="1521" style="width: 35px; color: rgba(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">@@ -1554,28 +1521,27 @@ Rv1996 T - Signal transduction mechanisms</td>
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1554
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<td class="diff-line-num new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1521
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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="plaintext">Rv1997 P ctpF Inorganic ion transport and metabolism </span>
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<td class="diff-line-num old_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1555
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<td class="diff-line-num new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1522
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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="plaintext">Rv1998c G - Carbohydrate transport and metabolism </span>
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<td class="diff-line-num old_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1556
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<td class="diff-line-num new_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1523
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="plaintext">Rv1999c E - Amino acid transport and metabolism </span>
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1557
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<td class="diff-line-num new_line old" data-linenumber="1524" style="width: 35px; color: rgba(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="LC1557" class="line" lang="plaintext">Rv2000 R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1558
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<td class="diff-line-num new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="plaintext">Rv2000 E - Amino acid transport and metabolism </span>
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<td class="diff-line-num new old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="plaintext">Rv2000 R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1559
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<td class="diff-line-num new_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="plaintext">Rv2001 I - Lipid transport and metabolism </span>
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<td class="diff-line-num old_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1560
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<td class="diff-line-num new_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1527
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<pre style="margin: 0;"> <span id="LC1527" class="line" lang="plaintext">Rv2002 R fabG3 General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1561
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<td class="diff-line-num new_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1528
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<pre style="margin: 0;"> <span id="LC1528" class="line" lang="plaintext">Rv2003c R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1562
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<td class="diff-line-num new_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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<pre style="margin: 0;"> <span id="LC1529" class="line" lang="plaintext">Rv2004c R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1563
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<td class="diff-line-num new_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="plaintext">Rv2004c S - Function unknown </span>
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1564
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1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="plaintext">Rv2005c T - Signal transduction mechanisms </span>
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1565
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<pre style="margin: 0;">-<span id="LC1565" class="line" lang="plaintext">Rv2006 R otsB1 General function prediction only </span>
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1566
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<pre style="margin: 0;">-<span id="LC1566" class="line" lang="plaintext">Rv2006 G otsB1 Carbohydrate transport and metabolism </span>
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1567
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1532
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="plaintext">Rv2006 G otsB1 Carbohydrate transport and metabolism </span>
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1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="plaintext">Rv2006 R otsB1 General function prediction only </span>
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1568
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1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="plaintext">Rv2007c C fdxA Energy production and conversion </span>
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1569
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<pre style="margin: 0;">-<span id="LC1569" class="line" lang="plaintext">Rv2008c R - General function prediction only </span>
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1570
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1535
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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="plaintext">Rv2008c J - Translation, ribosomal structure and biogenesis </span>
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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="plaintext">Rv2008c R - General function prediction only </span>
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1571
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1537
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<pre style="margin: 0;"> <span id="LC1537" class="line" lang="plaintext">Rv2009 K - Transcription </span>
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1572
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1538
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="plaintext">Rv2010 R - General function prediction only </span>
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1573
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1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="plaintext">Rv2011c K - Transcription </span>
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1574
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1540
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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="plaintext">Rv2012 R - General function prediction only </span>
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1575
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1541
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="plaintext">Rv2013 L - Replication, recombination and repair </span>
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1576
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<td class="diff-line-num new_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="plaintext">Rv2014 L - Replication, recombination and repair </span>
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1577
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<td class="diff-line-num new_line old" data-linenumber="1543" style="width: 35px; color: rgba(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="LC1577" class="line" lang="plaintext">Rv2017 K - Transcription </span>
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<td class="diff-line-num old_line" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1578
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<td class="diff-line-num new_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="plaintext">Rv2017 E - Amino acid transport and metabolism </span>
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1544
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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="plaintext">Rv2017 K - Transcription </span>
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1579
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<td class="diff-line-num new_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1545
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<pre style="margin: 0;"> <span id="LC1545" class="line" lang="plaintext">Rv2018 S - Function unknown </span>
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1580
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1546
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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="plaintext">Rv2020c R - General function prediction only </span>
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1581
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1547
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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="plaintext">Rv2021c K - Transcription </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1584" style="width: 35px; color: rgba(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="1550" style="width: 35px; color: rgba(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">@@ -1584,11 +1550,9 @@ Rv2024c R - General function prediction only</td>
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1584
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1550
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<pre style="margin: 0;"> <span id="LC1550" class="line" lang="plaintext">Rv2025c P - Inorganic ion transport and metabolism </span>
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1585
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1551
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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="plaintext">Rv2026c T - Signal transduction mechanisms </span>
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1586
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1552
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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="plaintext">Rv2027c T - Signal transduction mechanisms </span>
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1587
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<pre style="margin: 0;">-<span id="LC1587" class="line" lang="plaintext">Rv2027c T - Signal transduction mechanisms </span>
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1588
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1553
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="plaintext">Rv2028c T - Signal transduction mechanisms </span>
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1589
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1554
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<pre style="margin: 0;"> <span id="LC1554" class="line" lang="plaintext">Rv2029c G pfkB Carbohydrate transport and metabolism </span>
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1590
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1555
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="plaintext">Rv2030c R - General function prediction only </span>
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1591
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<pre style="margin: 0;">-<span id="LC1591" class="line" lang="plaintext">Rv2030c R - General function prediction only </span>
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1592
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1556
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<pre style="margin: 0;"> <span id="LC1556" class="line" lang="plaintext">Rv2031c O hspX Posttranslational modification, protein turnover, chaperones </span>
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1593
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1557
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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="plaintext">Rv2032 C acg Energy production and conversion </span>
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1594
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1558
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<pre style="margin: 0;"> <span id="LC1558" class="line" lang="plaintext">Rv2034 K - Transcription </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1601" style="width: 35px; color: rgba(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="1565" style="width: 35px; color: rgba(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">@@ -1601,10 +1565,8 @@ Rv2043c Q pncA Secondary metabolites biosynthesis, transport and catabolism</td>
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1601
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1565
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<pre style="margin: 0;"> <span id="LC1565" class="line" lang="plaintext">Rv2045c I lipT Lipid transport and metabolism </span>
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1602
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1566
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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="plaintext">Rv2046 Q lppI Secondary metabolites biosynthesis, transport and catabolism </span>
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1603
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1567
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="plaintext">Rv2047c G - Carbohydrate transport and metabolism </span>
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1604
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<pre style="margin: 0;">-<span id="LC1604" class="line" lang="plaintext">Rv2047c G - Carbohydrate transport and metabolism </span>
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1605
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1568
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="plaintext">Rv2048c Q pks12 Secondary metabolites biosynthesis, transport and catabolism </span>
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1606
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1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="plaintext">Rv2051c M ppm1 Cell wall/membrane/envelope biogenesis </span>
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1607
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<pre style="margin: 0;">-<span id="LC1607" class="line" lang="plaintext">Rv2051c M ppm1 Cell wall/membrane/envelope biogenesis </span>
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1608
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1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="plaintext">Rv2052c R - General function prediction only </span>
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1609
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1571
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="plaintext">Rv2054 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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1610
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1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="plaintext">Rv2055c J rpsR Translation, ribosomal structure and biogenesis </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1618,14 +1580,12 @@ Rv2062c H cobN Coenzyme transport and metabolism</td>
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1618
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1580
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<pre style="margin: 0;"> <span id="LC1580" class="line" lang="plaintext">Rv2064 P cobG Inorganic ion transport and metabolism </span>
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1619
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1581
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<pre style="margin: 0;"> <span id="LC1581" class="line" lang="plaintext">Rv2065 H cobH Coenzyme transport and metabolism </span>
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1620
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1582
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<pre style="margin: 0;"> <span id="LC1582" class="line" lang="plaintext">Rv2066 H cobI Coenzyme transport and metabolism </span>
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1621
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<pre style="margin: 0;">-<span id="LC1621" class="line" lang="plaintext">Rv2066 H cobI Coenzyme transport and metabolism </span>
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1622
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1583
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<pre style="margin: 0;"> <span id="LC1583" class="line" lang="plaintext">Rv2067c R - General function prediction only </span>
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1623
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1584
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<pre style="margin: 0;"> <span id="LC1584" class="line" lang="plaintext">Rv2068c V blaC Defense mechanisms </span>
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1624
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1585
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<pre style="margin: 0;"> <span id="LC1585" class="line" lang="plaintext">Rv2069 K sigC Transcription </span>
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1625
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1586
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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="plaintext">Rv2070c H cobK Coenzyme transport and metabolism </span>
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1626
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1587
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<pre style="margin: 0;"> <span id="LC1587" class="line" lang="plaintext">Rv2071c H cobM Coenzyme transport and metabolism </span>
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1627
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1588
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<pre style="margin: 0;"> <span id="LC1588" class="line" lang="plaintext">Rv2072c H cobL Coenzyme transport and metabolism </span>
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1628
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<pre style="margin: 0;">-<span id="LC1628" class="line" lang="plaintext">Rv2072c H cobL Coenzyme transport and metabolism </span>
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1629
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1589
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<pre style="margin: 0;"> <span id="LC1589" class="line" lang="plaintext">Rv2073c R - General function prediction only </span>
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1630
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1590
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<pre style="margin: 0;"> <span id="LC1590" class="line" lang="plaintext">Rv2086 L - Replication, recombination and repair </span>
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1631
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1591
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<pre style="margin: 0;"> <span id="LC1591" class="line" lang="plaintext">Rv2087 L - Replication, recombination and repair </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1640,7 +1600,6 @@ Rv2096c K - Transcription</td>
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1640
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1600
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<pre style="margin: 0;"> <span id="LC1600" class="line" lang="plaintext">Rv2101 L helZ Replication, recombination and repair </span>
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1641
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1601
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<pre style="margin: 0;"> <span id="LC1601" class="line" lang="plaintext">Rv2102 S - Function unknown </span>
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1642
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1602
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<pre style="margin: 0;"> <span id="LC1602" class="line" lang="plaintext">Rv2103c R - General function prediction only </span>
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1643
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<pre style="margin: 0;">-<span id="LC1643" class="line" lang="plaintext">Rv2103c R - General function prediction only </span>
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1644
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1603
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<pre style="margin: 0;"> <span id="LC1603" class="line" lang="plaintext">Rv2105 L - Replication, recombination and repair </span>
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1645
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1604
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<pre style="margin: 0;"> <span id="LC1604" class="line" lang="plaintext">Rv2106 L - Replication, recombination and repair </span>
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1646
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1605
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<pre style="margin: 0;"> <span id="LC1605" class="line" lang="plaintext">Rv2109c O prcA Posttranslational modification, protein turnover, chaperones </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1653" style="width: 35px; color: rgba(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="1612" style="width: 35px; color: rgba(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">@@ -1653,7 +1612,6 @@ Rv2120c S - Function unknown</td>
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1653
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1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="plaintext">Rv2121c E hisG Amino acid transport and metabolism </span>
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1654
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1613
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="plaintext">Rv2122c E hisE Amino acid transport and metabolism </span>
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1655
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1614
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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="plaintext">Rv2124c E metH Amino acid transport and metabolism </span>
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1656
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<pre style="margin: 0;">-<span id="LC1656" class="line" lang="plaintext">Rv2124c E metH Amino acid transport and metabolism </span>
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1657
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="plaintext">Rv2125 R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1658
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="plaintext">Rv2127 E ansP1 Amino acid transport and metabolism </span>
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1659
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1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="plaintext">Rv2129c R - General function prediction only </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1697" style="width: 35px; color: rgba(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="1655" style="width: 35px; color: rgba(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">@@ -1697,7 +1655,6 @@ Rv2187 I fadD15 Lipid transport and metabolism</td>
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1697
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1655
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<pre style="margin: 0;"> <span id="LC1655" class="line" lang="plaintext">Rv2188c M - Cell wall/membrane/envelope biogenesis </span>
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1698
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1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="plaintext">Rv2190c M - Cell wall/membrane/envelope biogenesis </span>
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1699
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1657
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<pre style="margin: 0;"> <span id="LC1657" class="line" lang="plaintext">Rv2191 L - Replication, recombination and repair </span>
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1700
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<pre style="margin: 0;">-<span id="LC1700" class="line" lang="plaintext">Rv2191 L - Replication, recombination and repair </span>
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1701
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1658
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<pre style="margin: 0;"> <span id="LC1658" class="line" lang="plaintext">Rv2192c E trpD Amino acid transport and metabolism </span>
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1702
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1659
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="plaintext">Rv2193 C ctaE Energy production and conversion </span>
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1703
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="plaintext">Rv2194 C qcrC Energy production and conversion </span>
</pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1715,7 +1672,6 @@ Rv2211c E gcvT Amino acid transport and metabolism</td>
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1715
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1672
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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="plaintext">Rv2212 T - Signal transduction mechanisms </span>
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1716
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1673
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<pre style="margin: 0;"> <span id="LC1673" class="line" lang="plaintext">Rv2213 E pepB Amino acid transport and metabolism </span>
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1717
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1674
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<pre style="margin: 0;"> <span id="LC1674" class="line" lang="plaintext">Rv2214c R ephD General function prediction only </span>
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1718
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<pre style="margin: 0;">-<span id="LC1718" class="line" lang="plaintext">Rv2214c R ephD General function prediction only </span>
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1719
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1675
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<pre style="margin: 0;"> <span id="LC1675" class="line" lang="plaintext">Rv2215 C dlaT Energy production and conversion </span>
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1720
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1676
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<pre style="margin: 0;"> <span id="LC1676" class="line" lang="plaintext">Rv2216 R - General function prediction only </span>
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1721
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1677
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<pre style="margin: 0;"> <span id="LC1677" class="line" lang="plaintext">Rv2217 H lipB Coenzyme transport and metabolism </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1684" style="width: 35px; color: rgba(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">@@ -1728,11 +1684,10 @@ Rv2224c R - General function prediction only</td>
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1728
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1684
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<pre style="margin: 0;"> <span id="LC1684" class="line" lang="plaintext">Rv2225 H panB Coenzyme transport and metabolism </span>
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1729
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1685
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<pre style="margin: 0;"> <span id="LC1685" class="line" lang="plaintext">Rv2226 S - Function unknown </span>
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1730
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1686
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<pre style="margin: 0;"> <span id="LC1686" class="line" lang="plaintext">Rv2227 S - Function unknown </span>
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1731
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<pre style="margin: 0;">-<span id="LC1731" class="line" lang="plaintext">Rv2228c L - Replication, recombination and repair </span>
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1732
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1687
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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="plaintext">Rv2228c G - Carbohydrate transport and metabolism </span>
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<td class="diff-line-num new old_line" data-linenumber="1733" style="width: 35px; color: rgba(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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1688
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<pre style="margin: 0;">+<span id="LC1688" class="line" lang="plaintext">Rv2228c L - Replication, recombination and repair </span>
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1733
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1689
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<pre style="margin: 0;"> <span id="LC1689" class="line" lang="plaintext">Rv2229c R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1734
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1690
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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="plaintext">Rv2230c S - Function unknown </span>
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1735
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<pre style="margin: 0;">-<span id="LC1735" class="line" lang="plaintext">Rv2230c S - Function unknown </span>
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1736
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1691
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="plaintext">Rv2231c E cobC Amino acid transport and metabolism </span>
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1737
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1692
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<pre style="margin: 0;"> <span id="LC1692" class="line" lang="plaintext">Rv2232 R - General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="1738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1738
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1693
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<pre style="margin: 0;"> <span id="LC1693" class="line" lang="plaintext">Rv2234 T ptpA Signal transduction mechanisms </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1748" style="width: 35px; color: rgba(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="1703" style="width: 35px; color: rgba(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">@@ -1748,8 +1703,8 @@ Rv2245 Q kasA Secondary metabolites biosynthesis, transport and catabolism</td>
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1748
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1703
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<pre style="margin: 0;"> <span id="LC1703" class="line" lang="plaintext">Rv2246 Q kasB Secondary metabolites biosynthesis, transport and catabolism </span>
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1749
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1704
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<pre style="margin: 0;"> <span id="LC1704" class="line" lang="plaintext">Rv2247 I accD6 Lipid transport and metabolism </span>
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1750
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1705
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<pre style="margin: 0;"> <span id="LC1705" class="line" lang="plaintext">Rv2249c C glpD1 Energy production and conversion </span>
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1751
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<pre style="margin: 0;">-<span id="LC1751" class="line" lang="plaintext">Rv2250c K - Transcription </span>
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1752
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1706
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<pre style="margin: 0;"> <span id="LC1706" class="line" lang="plaintext">Rv2250A C - Energy production and conversion </span>
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1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="plaintext">Rv2250c K - Transcription </span>
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1753
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1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="plaintext">Rv2251 C - Energy production and conversion </span>
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1754
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1709
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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="plaintext">Rv2252 R - General function prediction only </span>
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1755
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1710
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<pre style="margin: 0;"> <span id="LC1710" class="line" lang="plaintext">Rv2257c V - Defense mechanisms </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1847,7 +1802,6 @@ Rv2380c Q mbtE Secondary metabolites biosynthesis, transport and catabolism</td>
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1847
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1802
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<pre style="margin: 0;"> <span id="LC1802" class="line" lang="plaintext">Rv2381c Q mbtD Secondary metabolites biosynthesis, transport and catabolism </span>
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1848
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1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="plaintext">Rv2382c Q mbtC Secondary metabolites biosynthesis, transport and catabolism </span>
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1849
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1804
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<pre style="margin: 0;"> <span id="LC1804" class="line" lang="plaintext">Rv2383c Q mbtB Secondary metabolites biosynthesis, transport and catabolism </span>
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1850
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<pre style="margin: 0;">-<span id="LC1850" class="line" lang="plaintext">Rv2383c Q mbtB Secondary metabolites biosynthesis, transport and catabolism </span>
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1851
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1805
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<pre style="margin: 0;"> <span id="LC1805" class="line" lang="plaintext">Rv2384 Q mbtA Secondary metabolites biosynthesis, transport and catabolism </span>
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1852
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1806
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<pre style="margin: 0;"> <span id="LC1806" class="line" lang="plaintext">Rv2385 I mbtJ Lipid transport and metabolism </span>
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1853
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1807
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<pre style="margin: 0;"> <span id="LC1807" class="line" lang="plaintext">Rv2386c H mbtI Coenzyme transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1885,9 +1839,8 @@ Rv2426c R - General function prediction only</td>
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1885
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1839
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<pre style="margin: 0;"> <span id="LC1839" class="line" lang="plaintext">Rv2427c E proA Amino acid transport and metabolism </span>
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1886
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1840
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<pre style="margin: 0;"> <span id="LC1840" class="line" lang="plaintext">Rv2428 O ahpC Posttranslational modification, protein turnover, chaperones </span>
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1887
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1841
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<pre style="margin: 0;"> <span id="LC1841" class="line" lang="plaintext">Rv2429 S ahpD Function unknown </span>
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1888
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<pre style="margin: 0;">-<span id="LC1888" class="line" lang="plaintext">Rv2434c T - Signal transduction mechanisms </span>
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1889
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1842
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<pre style="margin: 0;"> <span id="LC1842" class="line" lang="plaintext">Rv2434c M - Cell wall/membrane/envelope biogenesis </span>
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1890
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<pre style="margin: 0;">-<span id="LC1890" class="line" lang="plaintext">Rv243<span class="idiff left right">5</span>c T - Signal transduction mechanisms </span>
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1843
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<pre style="margin: 0;">+<span id="LC1843" class="line" lang="plaintext">Rv243<span class="idiff left right">4</span>c T - Signal transduction mechanisms </span>
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1891
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1844
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<pre style="margin: 0;"> <span id="LC1844" class="line" lang="plaintext">Rv2435c T - Signal transduction mechanisms </span>
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1892
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1845
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<pre style="margin: 0;"> <span id="LC1845" class="line" lang="plaintext">Rv2436 G rbsK Carbohydrate transport and metabolism </span>
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1893
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1846
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<pre style="margin: 0;"> <span id="LC1846" class="line" lang="plaintext">Rv2437 O - Posttranslational modification, protein turnover, chaperones </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1859" style="width: 35px; color: rgba(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">@@ -1906,7 +1859,6 @@ Rv2449c S - Function unknown</td>
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1906
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1859
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<pre style="margin: 0;"> <span id="LC1859" class="line" lang="plaintext">Rv2453c H mobA Coenzyme transport and metabolism </span>
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1907
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1860
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<pre style="margin: 0;"> <span id="LC1860" class="line" lang="plaintext">Rv2454c C - Energy production and conversion </span>
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1908
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1861
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<pre style="margin: 0;"> <span id="LC1861" class="line" lang="plaintext">Rv2455c C - Energy production and conversion </span>
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1909
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<pre style="margin: 0;">-<span id="LC1909" class="line" lang="plaintext">Rv2455c C - Energy production and conversion </span>
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1910
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1862
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<pre style="margin: 0;"> <span id="LC1862" class="line" lang="plaintext">Rv2456c R - General function prediction only </span>
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1911
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1863
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<pre style="margin: 0;"> <span id="LC1863" class="line" lang="plaintext">Rv2457c O clpX Posttranslational modification, protein turnover, chaperones </span>
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1912
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1864
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<pre style="margin: 0;"> <span id="LC1864" class="line" lang="plaintext">Rv2458 E mmuM Amino acid transport and metabolism </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1929" style="width: 35px; color: rgba(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="1881" style="width: 35px; color: rgba(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">@@ -1929,13 +1881,13 @@ Rv2478c L - Replication, recombination and repair</td>
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1929
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1881
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<pre style="margin: 0;"> <span id="LC1881" class="line" lang="plaintext">Rv2479c L - Replication, recombination and repair </span>
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1930
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1882
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<pre style="margin: 0;"> <span id="LC1882" class="line" lang="plaintext">Rv2480c L - Replication, recombination and repair </span>
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1931
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1883
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<pre style="margin: 0;"> <span id="LC1883" class="line" lang="plaintext">Rv2482c I plsB2 Lipid transport and metabolism </span>
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1932
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<pre style="margin: 0;">-<span id="LC1932" class="line" lang="plaintext">Rv2483c I plsC Lipid transport and metabolism </span>
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1933
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1884
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<pre style="margin: 0;"> <span id="LC1884" class="line" lang="plaintext">Rv2483c E plsC Amino acid transport and metabolism </span>
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1885
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<pre style="margin: 0;">+<span id="LC1885" class="line" lang="plaintext">Rv2483c I plsC Lipid transport and metabolism </span>
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1934
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1886
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<pre style="margin: 0;"> <span id="LC1886" class="line" lang="plaintext">Rv2485c I lipQ Lipid transport and metabolism </span>
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1935
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<td class="diff-line-num new_line" data-linenumber="1887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1887
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<pre style="margin: 0;"> <span id="LC1887" class="line" lang="plaintext">Rv2486 I echA14 Lipid transport and metabolism </span>
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1936
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<pre style="margin: 0;">-<span id="LC1936" class="line" lang="plaintext">Rv2488c T - Signal transduction mechanisms </span>
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1937
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1888
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<pre style="margin: 0;"> <span id="LC1888" class="line" lang="plaintext">Rv2488c K - Transcription </span>
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1938
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1889
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<pre style="margin: 0;"> <span id="LC1889" class="line" lang="plaintext">Rv2488c R - General function prediction only </span>
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1890
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<pre style="margin: 0;">+<span id="LC1890" class="line" lang="plaintext">Rv2488c T - Signal transduction mechanisms </span>
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1939
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1891
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<pre style="margin: 0;"> <span id="LC1891" class="line" lang="plaintext">Rv2491 R - General function prediction only </span>
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1940
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1892
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<pre style="margin: 0;"> <span id="LC1892" class="line" lang="plaintext">Rv2492 F - Nucleotide transport and metabolism </span>
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1941
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1893
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<pre style="margin: 0;"> <span id="LC1893" class="line" lang="plaintext">Rv2494 R - General function prediction only </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1956" style="width: 35px; color: rgba(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="1908" style="width: 35px; color: rgba(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">@@ -1956,17 +1908,14 @@ Rv2509 R - General function prediction only</td>
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1956
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1908
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<pre style="margin: 0;"> <span id="LC1908" class="line" lang="plaintext">Rv2510c R - General function prediction only </span>
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1957
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1909
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<pre style="margin: 0;"> <span id="LC1909" class="line" lang="plaintext">Rv2511 A orn RNA processing and modification </span>
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1958
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1910
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<pre style="margin: 0;"> <span id="LC1910" class="line" lang="plaintext">Rv2512c L - Replication, recombination and repair </span>
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1959
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<pre style="margin: 0;">-<span id="LC1959" class="line" lang="plaintext">Rv2515c K - Transcription </span>
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1960
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1911
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<pre style="margin: 0;"> <span id="LC1911" class="line" lang="plaintext">Rv2515c E - Amino acid transport and metabolism </span>
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1912
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<pre style="margin: 0;">+<span id="LC1912" class="line" lang="plaintext">Rv2515c K - Transcription </span>
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1961
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1913
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<pre style="margin: 0;"> <span id="LC1913" class="line" lang="plaintext">Rv2518c S lppS Function unknown </span>
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1962
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<td class="diff-line-num new_line" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1914
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<pre style="margin: 0;"> <span id="LC1914" class="line" lang="plaintext">Rv2521 O bcp Posttranslational modification, protein turnover, chaperones </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1963
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<td class="diff-line-num new_line" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1915
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<pre style="margin: 0;"> <span id="LC1915" class="line" lang="plaintext">Rv2522c E - Amino acid transport and metabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1964
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<td class="diff-line-num new_line" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1916
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<pre style="margin: 0;"> <span id="LC1916" class="line" lang="plaintext">Rv2523c I acpS Lipid transport and metabolism </span>
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<td class="diff-line-num old old_line" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1965
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<td class="diff-line-num new_line old" data-linenumber="1917" style="width: 35px; color: rgba(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="LC1965" class="line" lang="plaintext">Rv2524c Q fas Secondary metabolites biosynthesis, transport and catabolism </span>
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<td class="diff-line-num old old_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1966
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<td class="diff-line-num new_line old" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC1966" class="line" lang="plaintext">Rv2524c I fas Lipid transport and metabolism </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1967
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<td class="diff-line-num new_line old" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC1967" class="line" lang="plaintext">Rv2524c I fas Lipid transport and metabolism </span>
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<td class="diff-line-num old old_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1968
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<td class="diff-line-num new_line old" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC1968" class="line" lang="plaintext">Rv2524c I fas Lipid transport and metabolism </span>
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<td class="diff-line-num old_line" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1969
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<td class="diff-line-num new_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1917
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<pre style="margin: 0;"> <span id="LC1917" class="line" lang="plaintext">Rv2524c I fas Lipid transport and metabolism </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1918
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<pre style="margin: 0;">+<span id="LC1918" class="line" lang="plaintext">Rv2524c Q fas Secondary metabolites biosynthesis, transport and catabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1970
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<td class="diff-line-num new_line" data-linenumber="1919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1919
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<pre style="margin: 0;"> <span id="LC1919" class="line" lang="plaintext">Rv2527 R - General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1971
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<td class="diff-line-num new_line" data-linenumber="1920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1920
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<pre style="margin: 0;"> <span id="LC1920" class="line" lang="plaintext">Rv2528c V mrr Defense mechanisms </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1972
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<td class="diff-line-num new_line" data-linenumber="1921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1921
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<pre style="margin: 0;"> <span id="LC1921" class="line" lang="plaintext">Rv2529 L - Replication, recombination and repair </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1993" style="width: 35px; color: rgba(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="1942" style="width: 35px; color: rgba(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">@@ -1993,12 +1942,11 @@ Rv2559c L - Replication, recombination and repair</td>
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<td class="diff-line-num old_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1993
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<td class="diff-line-num new_line" data-linenumber="1942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1942
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<pre style="margin: 0;"> <span id="LC1942" class="line" lang="plaintext">Rv2561 E - Amino acid transport and metabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1994
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<td class="diff-line-num new_line" data-linenumber="1943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1943
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1943" class="line" lang="plaintext">Rv2563 V - Defense mechanisms </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1995
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<td class="diff-line-num new_line" data-linenumber="1944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1944
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1944" class="line" lang="plaintext">Rv2564 V glnQ Defense mechanisms </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1996
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<td class="diff-line-num new_line old" data-linenumber="1945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC1996" class="line" lang="plaintext">Rv2565 T - Signal transduction mechanisms </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1997
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<td class="diff-line-num new_line" data-linenumber="1945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1945
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1945" class="line" lang="plaintext">Rv2565 R - General function prediction only </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1946
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<pre style="margin: 0;">+<span id="LC1946" class="line" lang="plaintext">Rv2565 T - Signal transduction mechanisms </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1998
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<td class="diff-line-num new_line" data-linenumber="1947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1947
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1947" class="line" lang="plaintext">Rv2566 E - Amino acid transport and metabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1999
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<td class="diff-line-num new_line" data-linenumber="1948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1948
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1948" class="line" lang="plaintext">Rv2566 S - Function unknown </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2000
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<td class="diff-line-num new_line" data-linenumber="1949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1949
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<pre style="margin: 0;"> <span id="LC1949" class="line" lang="plaintext">Rv2567 S - Function unknown </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2001
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<td class="diff-line-num new_line old" data-linenumber="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC2001" class="line" lang="plaintext">Rv2567 S - Function unknown </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2002
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<td class="diff-line-num new_line" data-linenumber="1950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1950
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1950" class="line" lang="plaintext">Rv2568c S - Function unknown </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2003
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<td class="diff-line-num new_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1951
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1951" class="line" lang="plaintext">Rv2569c E - Amino acid transport and metabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2004
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<td class="diff-line-num new_line" data-linenumber="1952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1952
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1952" class="line" lang="plaintext">Rv2570 S - Function unknown </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2006" style="width: 35px; color: rgba(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="1954" style="width: 35px; color: rgba(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">@@ -2006,8 +1954,8 @@ Rv2571c S - Function unknown</td>
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<td class="diff-line-num old_line" data-linenumber="2006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2006
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<td class="diff-line-num new_line" data-linenumber="1954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1954
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<pre style="margin: 0;"> <span id="LC1954" class="line" lang="plaintext">Rv2572c J aspS Translation, ribosomal structure and biogenesis </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2007
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<td class="diff-line-num new_line" data-linenumber="1955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1955
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<pre style="margin: 0;"> <span id="LC1955" class="line" lang="plaintext">Rv2573 H - Coenzyme transport and metabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2008
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<td class="diff-line-num new_line" data-linenumber="1956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1956
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<pre style="margin: 0;"> <span id="LC1956" class="line" lang="plaintext">Rv2575 R - General function prediction only </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2009
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<td class="diff-line-num new_line old" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC2009" class="line" lang="plaintext">Rv2577 R - General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2010
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<td class="diff-line-num new_line" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="plaintext">Rv2577 P - Inorganic ion transport and metabolism </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1958
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<pre style="margin: 0;">+<span id="LC1958" class="line" lang="plaintext">Rv2577 R - General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2011
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<td class="diff-line-num new_line" data-linenumber="1959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1959
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<pre style="margin: 0;"> <span id="LC1959" class="line" lang="plaintext">Rv2578c L - Replication, recombination and repair </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2012
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<td class="diff-line-num new_line" data-linenumber="1960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1960
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<pre style="margin: 0;"> <span id="LC1960" class="line" lang="plaintext">Rv2579 R dhaA General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2013
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<td class="diff-line-num new_line" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1961
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1961" class="line" lang="plaintext">Rv2580c J hisS Translation, ribosomal structure and biogenesis </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2038" style="width: 35px; color: rgba(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="1986" style="width: 35px; color: rgba(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">@@ -2038,8 +1986,8 @@ Rv2610c M pimA Cell wall/membrane/envelope biogenesis</td>
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<td class="diff-line-num old_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2038
</td>
<td class="diff-line-num new_line" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1986
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<pre style="margin: 0;"> <span id="LC1986" class="line" lang="plaintext">Rv2611c M - Cell wall/membrane/envelope biogenesis </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2039
</td>
<td class="diff-line-num new_line" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1987
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1987" class="line" lang="plaintext">Rv2612c I pgsA1 Lipid transport and metabolism </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2040
</td>
<td class="diff-line-num new_line" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1988
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1988" class="line" lang="plaintext">Rv2613c R - General function prediction only </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2041
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<td class="diff-line-num new_line old" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC2041" class="line" lang="plaintext">Rv2614c J thrS Translation, ribosomal structure and biogenesis </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2042
</td>
<td class="diff-line-num new_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1989
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1989" class="line" lang="plaintext">Rv2614A G - Carbohydrate transport and metabolism </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1990
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1990" class="line" lang="plaintext">Rv2614c J thrS Translation, ribosomal structure and biogenesis </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2043
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<td class="diff-line-num new_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1991
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1991" class="line" lang="plaintext">Rv2616 S - Function unknown </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2044
</td>
<td class="diff-line-num new_line" data-linenumber="1992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1992
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1992" class="line" lang="plaintext">Rv2618 K - Transcription </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2045
</td>
<td class="diff-line-num new_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1993
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1993" class="line" lang="plaintext">Rv2619c S - Function unknown </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2048" style="width: 35px; color: rgba(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="1996" style="width: 35px; color: rgba(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">@@ -2048,10 +1996,9 @@ Rv2622 R - General function prediction only</td>
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<td class="diff-line-num old_line" data-linenumber="2048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2048
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<td class="diff-line-num new_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1996
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1996" class="line" lang="plaintext">Rv2623 T TB31.7 Signal transduction mechanisms </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2049
</td>
<td class="diff-line-num new_line" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1997
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1997" class="line" lang="plaintext">Rv2624c T - Signal transduction mechanisms </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2050
</td>
<td class="diff-line-num new_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1998
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1998" class="line" lang="plaintext">Rv2625c R - General function prediction only </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2051
</td>
<td class="diff-line-num new_line old" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2051" class="line" lang="plaintext">Rv2625c R - General function prediction only </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2052
</td>
<td class="diff-line-num new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1999
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1999" class="line" lang="plaintext">Rv2626c R - General function prediction only </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2053
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<pre style="margin: 0;">-<span id="LC2053" class="line" lang="plaintext">Rv2629 L - Replication, recombination and repair </span>
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2054
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2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="plaintext">Rv2629 J - Translation, ribosomal structure and biogenesis </span>
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<td class="diff-line-num new new_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2001
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<pre style="margin: 0;">+<span id="LC2001" class="line" lang="plaintext">Rv2629 L - Replication, recombination and repair </span>
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2055
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2002
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<pre style="margin: 0;"> <span id="LC2002" class="line" lang="plaintext">Rv2630 S - Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="2056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2056
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2003
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<pre style="margin: 0;"> <span id="LC2003" class="line" lang="plaintext">Rv2631 S - Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="2057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2057
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<td class="diff-line-num new_line" data-linenumber="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2004
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<pre style="margin: 0;"> <span id="LC2004" class="line" lang="plaintext">Rv2636 V - Defense mechanisms </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2061" style="width: 35px; color: rgba(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="2008" style="width: 35px; color: rgba(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">@@ -2061,8 +2008,8 @@ Rv2639c S - Function unknown</td>
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2061
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2008
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<pre style="margin: 0;"> <span id="LC2008" class="line" lang="plaintext">Rv2640c K - Transcription </span>
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<td class="diff-line-num old_line" data-linenumber="2062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2062
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<td class="diff-line-num new_line" data-linenumber="2009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2009
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<pre style="margin: 0;"> <span id="LC2009" class="line" lang="plaintext">Rv2641 E cadI Amino acid transport and metabolism </span>
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<td class="diff-line-num old_line" data-linenumber="2063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2063
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<td class="diff-line-num new_line" data-linenumber="2010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2010
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<pre style="margin: 0;"> <span id="LC2010" class="line" lang="plaintext">Rv2642 K - Transcription </span>
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<td class="diff-line-num old old_line" data-linenumber="2064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2064
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<td class="diff-line-num new_line old" data-linenumber="2011" style="width: 35px; color: rgba(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="LC2064" class="line" lang="plaintext">Rv2643 T arsC Signal transduction mechanisms </span>
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<td class="diff-line-num old_line" data-linenumber="2065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2065
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2011
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<pre style="margin: 0;"> <span id="LC2011" class="line" lang="plaintext">Rv2643 P arsC Inorganic ion transport and metabolism </span>
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<td class="diff-line-num new old_line" data-linenumber="2066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2012
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<pre style="margin: 0;">+<span id="LC2012" class="line" lang="plaintext">Rv2643 T arsC Signal transduction mechanisms </span>
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<td class="diff-line-num old_line" data-linenumber="2066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2066
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<td class="diff-line-num new_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2013
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<pre style="margin: 0;"> <span id="LC2013" class="line" lang="plaintext">Rv2646 L - Replication, recombination and repair </span>
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<td class="diff-line-num old_line" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2067
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<td class="diff-line-num new_line" data-linenumber="2014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2014
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<pre style="margin: 0;"> <span id="LC2014" class="line" lang="plaintext">Rv2648 L - Replication, recombination and repair </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2068
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2015
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<pre style="margin: 0;"> <span id="LC2015" class="line" lang="plaintext">Rv2649 L - Replication, recombination and repair </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2120" style="width: 35px; color: rgba(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="2067" style="width: 35px; color: rgba(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">@@ -2120,7 +2067,6 @@ Rv2733c J - Translation, ribosomal structure and biogenesis</td>
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2120
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2067
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="plaintext">Rv2734 S - Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2121
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2068
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<pre style="margin: 0;"> <span id="LC2068" class="line" lang="plaintext">Rv2736c R recX General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="2122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2122
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<td class="diff-line-num new_line" data-linenumber="2069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2069
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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="plaintext">Rv2737c L recA Replication, recombination and repair </span>
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2123
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<td class="diff-line-num new_line old" data-linenumber="2070" style="width: 35px; color: rgba(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="LC2123" class="line" lang="plaintext">Rv2737c L recA Replication, recombination and repair </span>
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2124
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2070
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<pre style="margin: 0;"> <span id="LC2070" class="line" lang="plaintext">Rv2739c C - Energy production and conversion </span>
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<td class="diff-line-num old_line" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2125
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<td class="diff-line-num new_line" data-linenumber="2071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2071
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<pre style="margin: 0;"> <span id="LC2071" class="line" lang="plaintext">Rv2740 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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2126
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<td class="diff-line-num new_line" data-linenumber="2072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2072
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<pre style="margin: 0;"> <span id="LC2072" class="line" lang="plaintext">Rv2744c T 35kd_ag Signal transduction mechanisms </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2202" style="width: 35px; color: rgba(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="2148" style="width: 35px; color: rgba(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">@@ -2202,11 +2148,9 @@ Rv2842c S - Function unknown</td>
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2202
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2148
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<pre style="margin: 0;"> <span id="LC2148" class="line" lang="plaintext">Rv2845c J proS Translation, ribosomal structure and biogenesis </span>
</pre>
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2203
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2149
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<pre style="margin: 0;"> <span id="LC2149" class="line" lang="plaintext">Rv2846c R efpA General function prediction only </span>
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2204
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2150
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<pre style="margin: 0;"> <span id="LC2150" class="line" lang="plaintext">Rv2847c H cysG Coenzyme transport and metabolism </span>
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2205
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<pre style="margin: 0;">-<span id="LC2205" class="line" lang="plaintext">Rv2847c H cysG Coenzyme transport and metabolism </span>
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2206
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2151
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<pre style="margin: 0;"> <span id="LC2151" class="line" lang="plaintext">Rv2848c H cobB Coenzyme transport and metabolism </span>
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2207
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2152
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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="plaintext">Rv2849c H cobO Coenzyme transport and metabolism </span>
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2208
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2153
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<pre style="margin: 0;"> <span id="LC2153" class="line" lang="plaintext">Rv2850c H - Coenzyme transport and metabolism </span>
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2209
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<pre style="margin: 0;">-<span id="LC2209" class="line" lang="plaintext">Rv2850c H - Coenzyme transport and metabolism </span>
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2210
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2154
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<pre style="margin: 0;"> <span id="LC2154" class="line" lang="plaintext">Rv2851c R - General function prediction only </span>
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2211
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2155
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<pre style="margin: 0;"> <span id="LC2155" class="line" lang="plaintext">Rv2852c R mqo General function prediction only </span>
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2212
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2156
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<pre style="margin: 0;"> <span id="LC2156" class="line" lang="plaintext">Rv2854 I - Lipid transport and metabolism </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2269" style="width: 35px; color: rgba(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="2213" style="width: 35px; color: rgba(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">@@ -2269,8 +2213,8 @@ Rv2918c O glnD Posttranslational modification, protein turnover, chaperones</td>
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2269
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2213
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<pre style="margin: 0;"> <span id="LC2213" class="line" lang="plaintext">Rv2919c E glnB Amino acid transport and metabolism </span>
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2270
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2214
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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="plaintext">Rv2920c P amt Inorganic ion transport and metabolism </span>
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2271
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2215
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<pre style="margin: 0;"> <span id="LC2215" class="line" lang="plaintext">Rv2921c U ftsY Intracellular trafficking, secretion, and vesicular transport </span>
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2272
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<pre style="margin: 0;">-<span id="LC2272" class="line" lang="plaintext">Rv2922c D smc Cell cycle control, cell division, chromosome partitioning </span>
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2273
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2216
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<pre style="margin: 0;"> <span id="LC2216" class="line" lang="plaintext">Rv2922A C acyP Energy production and conversion </span>
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2217
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<pre style="margin: 0;">+<span id="LC2217" class="line" lang="plaintext">Rv2922c D smc Cell cycle control, cell division, chromosome partitioning </span>
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2274
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2218
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<pre style="margin: 0;"> <span id="LC2218" class="line" lang="plaintext">Rv2923c O - Posttranslational modification, protein turnover, chaperones </span>
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2275
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2219
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<pre style="margin: 0;"> <span id="LC2219" class="line" lang="plaintext">Rv2924c L fpg Replication, recombination and repair </span>
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2276
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2220
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<pre style="margin: 0;"> <span id="LC2220" class="line" lang="plaintext">Rv2925c K rnc Transcription </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2283" style="width: 35px; color: rgba(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="2227" style="width: 35px; color: rgba(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">@@ -2283,7 +2227,6 @@ Rv2932 Q ppsB Secondary metabolites biosynthesis, transport and catabolism</td>
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2283
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2227
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<pre style="margin: 0;"> <span id="LC2227" class="line" lang="plaintext">Rv2933 Q ppsC Secondary metabolites biosynthesis, transport and catabolism </span>
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2284
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2228
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<pre style="margin: 0;"> <span id="LC2228" class="line" lang="plaintext">Rv2934 Q ppsD Secondary metabolites biosynthesis, transport and catabolism </span>
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2285
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2229
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<pre style="margin: 0;"> <span id="LC2229" class="line" lang="plaintext">Rv2935 Q ppsE Secondary metabolites biosynthesis, transport and catabolism </span>
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2286
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<pre style="margin: 0;">-<span id="LC2286" class="line" lang="plaintext">Rv2935 Q ppsE Secondary metabolites biosynthesis, transport and catabolism </span>
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2287
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2230
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<pre style="margin: 0;"> <span id="LC2230" class="line" lang="plaintext">Rv2936 V drrA Defense mechanisms </span>
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2288
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2231
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<pre style="margin: 0;"> <span id="LC2231" class="line" lang="plaintext">Rv2937 V drrB Defense mechanisms </span>
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2289
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2232
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<pre style="margin: 0;"> <span id="LC2232" class="line" lang="plaintext">Rv2938 V drrC Defense mechanisms </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2297" style="width: 35px; color: rgba(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="2240" style="width: 35px; color: rgba(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">@@ -2297,7 +2240,6 @@ Rv2944 L - Replication, recombination and repair</td>
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2297
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2240
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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="plaintext">Rv2946c Q pks1 Secondary metabolites biosynthesis, transport and catabolism </span>
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2298
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2241
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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="plaintext">Rv2947c Q pks15 Secondary metabolites biosynthesis, transport and catabolism </span>
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2299
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2242
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<pre style="margin: 0;"> <span id="LC2242" class="line" lang="plaintext">Rv2948c Q fadD22 Secondary metabolites biosynthesis, transport and catabolism </span>
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2300
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<pre style="margin: 0;">-<span id="LC2300" class="line" lang="plaintext">Rv2948c Q fadD22 Secondary metabolites biosynthesis, transport and catabolism </span>
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2301
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2243
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<pre style="margin: 0;"> <span id="LC2243" class="line" lang="plaintext">Rv2949c H - Coenzyme transport and metabolism </span>
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2302
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2244
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<pre style="margin: 0;"> <span id="LC2244" class="line" lang="plaintext">Rv2950c Q fadD29 Secondary metabolites biosynthesis, transport and catabolism </span>
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2303
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2245
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<pre style="margin: 0;"> <span id="LC2245" class="line" lang="plaintext">Rv2951c C - Energy production and conversion </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2318" style="width: 35px; color: rgba(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="2260" style="width: 35px; color: rgba(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">@@ -2318,8 +2260,8 @@ Rv2966c L - Replication, recombination and repair</td>
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2318
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2260
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<pre style="margin: 0;"> <span id="LC2260" class="line" lang="plaintext">Rv2967c C pca Energy production and conversion </span>
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2319
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2261
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<pre style="margin: 0;"> <span id="LC2261" class="line" lang="plaintext">Rv2968c S - Function unknown </span>
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2320
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2262
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<pre style="margin: 0;"> <span id="LC2262" class="line" lang="plaintext">Rv2969c O - Posttranslational modification, protein turnover, chaperones </span>
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2321
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<pre style="margin: 0;">-<span id="LC2321" class="line" lang="plaintext">Rv2970c I lipN Lipid transport and metabolism </span>
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2322
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2263
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<pre style="margin: 0;"> <span id="LC2263" class="line" lang="plaintext">Rv2970A R - General function prediction only </span>
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2264
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<pre style="margin: 0;">+<span id="LC2264" class="line" lang="plaintext">Rv2970c I lipN Lipid transport and metabolism </span>
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2323
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2265
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<pre style="margin: 0;"> <span id="LC2265" class="line" lang="plaintext">Rv2971 R - General function prediction only </span>
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2324
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2266
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<pre style="margin: 0;"> <span id="LC2266" class="line" lang="plaintext">Rv2973c K recG Transcription </span>
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2325
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2267
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<pre style="margin: 0;"> <span id="LC2267" class="line" lang="plaintext">Rv2974c R - General function prediction only </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2414" style="width: 35px; color: rgba(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="2356" style="width: 35px; color: rgba(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">@@ -2414,8 +2356,8 @@ Rv3074 V - Defense mechanisms</td>
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2414
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2356
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<pre style="margin: 0;"> <span id="LC2356" class="line" lang="plaintext">Rv3075c G - Carbohydrate transport and metabolism </span>
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2415
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2357
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<pre style="margin: 0;"> <span id="LC2357" class="line" lang="plaintext">Rv3077 P - Inorganic ion transport and metabolism </span>
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2416
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2358
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<pre style="margin: 0;"> <span id="LC2358" class="line" lang="plaintext">Rv3079c C - Energy production and conversion </span>
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2417
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<pre style="margin: 0;">-<span id="LC2417" class="line" lang="plaintext">Rv3080c L pknK Replication, recombination and repair </span>
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2418
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2359
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<pre style="margin: 0;"> <span id="LC2359" class="line" lang="plaintext">Rv3080c K pknK Transcription </span>
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2360
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<pre style="margin: 0;">+<span id="LC2360" class="line" lang="plaintext">Rv3080c L pknK Replication, recombination and repair </span>
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2419
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2361
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<pre style="margin: 0;"> <span id="LC2361" class="line" lang="plaintext">Rv3082c K virS Transcription </span>
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2420
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2362
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<pre style="margin: 0;"> <span id="LC2362" class="line" lang="plaintext">Rv3083 P - Inorganic ion transport and metabolism </span>
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2421
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2363
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<pre style="margin: 0;"> <span id="LC2363" class="line" lang="plaintext">Rv3084 I lipR Lipid transport and metabolism </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2393" style="width: 35px; color: rgba(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">@@ -2451,7 +2393,6 @@ Rv3120 R - General function prediction only</td>
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2451
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2393
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<pre style="margin: 0;"> <span id="LC2393" class="line" lang="plaintext">Rv3121 Q cyp141 Secondary metabolites biosynthesis, transport and catabolism </span>
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2452
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2394
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<pre style="margin: 0;"> <span id="LC2394" class="line" lang="plaintext">Rv3124 T - Signal transduction mechanisms </span>
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2453
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2395
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<pre style="margin: 0;"> <span id="LC2395" class="line" lang="plaintext">Rv3132c T devS Signal transduction mechanisms </span>
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2454
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<pre style="margin: 0;">-<span id="LC2454" class="line" lang="plaintext">Rv3132c T devS Signal transduction mechanisms </span>
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2455
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2396
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<pre style="margin: 0;"> <span id="LC2396" class="line" lang="plaintext">Rv3133c K devR Transcription </span>
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2456
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2397
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<pre style="margin: 0;"> <span id="LC2397" class="line" lang="plaintext">Rv3134c T - Signal transduction mechanisms </span>
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2457
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2398
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<pre style="margin: 0;"> <span id="LC2398" class="line" lang="plaintext">Rv3137 G - Carbohydrate transport and metabolism </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2489" style="width: 35px; color: rgba(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">@@ -2489,8 +2430,8 @@ Rv3176c R mesT General function prediction only</td>
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2489
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2430
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<pre style="margin: 0;"> <span id="LC2430" class="line" lang="plaintext">Rv3177 R - General function prediction only </span>
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2490
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2431
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<pre style="margin: 0;"> <span id="LC2431" class="line" lang="plaintext">Rv3179 R - General function prediction only </span>
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2491
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2432
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<pre style="margin: 0;"> <span id="LC2432" class="line" lang="plaintext">Rv3180c R - General function prediction only </span>
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2492
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<pre style="margin: 0;">-<span id="LC2492" class="line" lang="plaintext">Rv3181c K - Transcription </span>
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2493
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2433
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<pre style="margin: 0;"> <span id="LC2433" class="line" lang="plaintext">Rv3181c D - Cell cycle control, cell division, chromosome partitioning </span>
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2434
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<pre style="margin: 0;">+<span id="LC2434" class="line" lang="plaintext">Rv3181c K - Transcription </span>
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2494
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2435
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<pre style="margin: 0;"> <span id="LC2435" class="line" lang="plaintext">Rv3182 S - Function unknown </span>
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2495
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2436
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<pre style="margin: 0;"> <span id="LC2436" class="line" lang="plaintext">Rv3183 K - Transcription </span>
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2496
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2437
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<pre style="margin: 0;"> <span id="LC2437" class="line" lang="plaintext">Rv3184 L - Replication, recombination and repair </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2503,13 +2444,11 @@ Rv3193c S - Function unknown</td>
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2503
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2444
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<pre style="margin: 0;"> <span id="LC2444" class="line" lang="plaintext">Rv3194c T - Signal transduction mechanisms </span>
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2504
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2445
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<pre style="margin: 0;"> <span id="LC2445" class="line" lang="plaintext">Rv3195 S - Function unknown </span>
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2505
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2446
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<pre style="margin: 0;"> <span id="LC2446" class="line" lang="plaintext">Rv3197 R - General function prediction only </span>
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2506
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<pre style="margin: 0;">-<span id="LC2506" class="line" lang="plaintext">Rv3198c L uvrD2 Replication, recombination and repair </span>
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2507
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2447
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<pre style="margin: 0;"> <span id="LC2447" class="line" lang="plaintext">Rv3198A O - Posttranslational modification, protein turnover, chaperones </span>
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2448
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<pre style="margin: 0;">+<span id="LC2448" class="line" lang="plaintext">Rv3198c L uvrD2 Replication, recombination and repair </span>
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2508
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2449
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<pre style="margin: 0;"> <span id="LC2449" class="line" lang="plaintext">Rv3199c L nudC Replication, recombination and repair </span>
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2509
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2450
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<pre style="margin: 0;"> <span id="LC2450" class="line" lang="plaintext">Rv3200c P - Inorganic ion transport and metabolism </span>
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2510
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2451
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<pre style="margin: 0;"> <span id="LC2451" class="line" lang="plaintext">Rv3201c L - Replication, recombination and repair </span>
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2511
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<pre style="margin: 0;">-<span id="LC2511" class="line" lang="plaintext">Rv3201c L - Replication, recombination and repair </span>
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2512
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<pre style="margin: 0;">-<span id="LC2512" class="line" lang="plaintext">Rv3202c L - Replication, recombination and repair </span>
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2513
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2452
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<pre style="margin: 0;"> <span id="LC2452" class="line" lang="plaintext">Rv3202c L - Replication, recombination and repair </span>
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2514
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2453
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<pre style="margin: 0;"> <span id="LC2453" class="line" lang="plaintext">Rv3203 R lipV General function prediction only </span>
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2515
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2454
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<pre style="margin: 0;"> <span id="LC2454" class="line" lang="plaintext">Rv3204 L - Replication, recombination and repair </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2523" style="width: 35px; color: rgba(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="2462" style="width: 35px; color: rgba(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">@@ -2523,8 +2462,8 @@ Rv3215 Q entC Secondary metabolites biosynthesis, transport and catabolism</td>
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2523
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2462
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<pre style="margin: 0;"> <span id="LC2462" class="line" lang="plaintext">Rv3216 R - General function prediction only </span>
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2524
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2463
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<pre style="margin: 0;"> <span id="LC2463" class="line" lang="plaintext">Rv3218 R - General function prediction only </span>
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2525
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2464
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<pre style="margin: 0;"> <span id="LC2464" class="line" lang="plaintext">Rv3220c T - Signal transduction mechanisms </span>
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2526
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<pre style="margin: 0;">-<span id="LC2526" class="line" lang="plaintext">Rv3221c I TB7.3 Lipid transport and metabolism </span>
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2527
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2465
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<pre style="margin: 0;"> <span id="LC2465" class="line" lang="plaintext">Rv3221A P - Inorganic ion transport and metabolism </span>
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2466
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<pre style="margin: 0;">+<span id="LC2466" class="line" lang="plaintext">Rv3221c I TB7.3 Lipid transport and metabolism </span>
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2528
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2467
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<pre style="margin: 0;"> <span id="LC2467" class="line" lang="plaintext">Rv3223c K sigH Transcription </span>
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2529
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2468
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<pre style="margin: 0;"> <span id="LC2468" class="line" lang="plaintext">Rv3224 R - General function prediction only </span>
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2530
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2469
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<pre style="margin: 0;"> <span id="LC2469" class="line" lang="plaintext">Rv3224B S - Function unknown </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2541" style="width: 35px; color: rgba(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="2480" style="width: 35px; color: rgba(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">@@ -2541,7 +2480,6 @@ Rv3237c P - Inorganic ion transport and metabolism</td>
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2541
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2480
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<pre style="margin: 0;"> <span id="LC2480" class="line" lang="plaintext">Rv3238c O - Posttranslational modification, protein turnover, chaperones </span>
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2542
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2481
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<pre style="margin: 0;"> <span id="LC2481" class="line" lang="plaintext">Rv3239c R - General function prediction only </span>
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2543
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2482
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<pre style="margin: 0;"> <span id="LC2482" class="line" lang="plaintext">Rv3239c T - Signal transduction mechanisms </span>
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2544
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<pre style="margin: 0;">-<span id="LC2544" class="line" lang="plaintext">Rv3239c R - General function prediction only </span>
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2545
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2483
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<pre style="margin: 0;"> <span id="LC2483" class="line" lang="plaintext">Rv3240c U secA1 Intracellular trafficking, secretion, and vesicular transport </span>
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2484
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<pre style="margin: 0;"> <span id="LC2484" class="line" lang="plaintext">Rv3241c J - Translation, ribosomal structure and biogenesis </span>
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2547
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2485
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<pre style="margin: 0;"> <span id="LC2485" class="line" lang="plaintext">Rv3242c R - General function prediction only </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2567,7 +2505,6 @@ Rv3267 K - Transcription</td>
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2567
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2505
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<pre style="margin: 0;"> <span id="LC2505" class="line" lang="plaintext">Rv3270 P ctpC Inorganic ion transport and metabolism </span>
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2568
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2506
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<pre style="margin: 0;"> <span id="LC2506" class="line" lang="plaintext">Rv3272 C - Energy production and conversion </span>
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2569
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2507
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<pre style="margin: 0;"> <span id="LC2507" class="line" lang="plaintext">Rv3273 P - Inorganic ion transport and metabolism </span>
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2570
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<pre style="margin: 0;">-<span id="LC2570" class="line" lang="plaintext">Rv3273 P - Inorganic ion transport and metabolism </span>
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2571
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2508
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<pre style="margin: 0;"> <span id="LC2508" class="line" lang="plaintext">Rv3274c I fadE25 Lipid transport and metabolism </span>
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2572
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2509
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<pre style="margin: 0;"> <span id="LC2509" class="line" lang="plaintext">Rv3275c F purE Nucleotide transport and metabolism </span>
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2573
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2510
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<pre style="margin: 0;"> <span id="LC2510" class="line" lang="plaintext">Rv3276c F purK Nucleotide transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2610,12 +2547,11 @@ Rv3319 C sdhB Energy production and conversion</td>
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2610
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2547
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<pre style="margin: 0;"> <span id="LC2547" class="line" lang="plaintext">Rv3320c R - General function prediction only </span>
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2611
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2548
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<pre style="margin: 0;"> <span id="LC2548" class="line" lang="plaintext">Rv3322c R - General function prediction only </span>
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2612
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2549
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<pre style="margin: 0;"> <span id="LC2549" class="line" lang="plaintext">Rv3323c H moaX Coenzyme transport and metabolism </span>
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2613
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<pre style="margin: 0;">-<span id="LC2613" class="line" lang="plaintext">Rv3323c H moaX Coenzyme transport and metabolism </span>
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2614
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2550
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<pre style="margin: 0;"> <span id="LC2550" class="line" lang="plaintext">Rv3324c H moaC Coenzyme transport and metabolism </span>
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2615
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2551
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<pre style="margin: 0;"> <span id="LC2551" class="line" lang="plaintext">Rv3325 L - Replication, recombination and repair </span>
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2616
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2552
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<pre style="margin: 0;"> <span id="LC2552" class="line" lang="plaintext">Rv3326 L - Replication, recombination and repair </span>
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2617
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<pre style="margin: 0;">-<span id="LC2617" class="line" lang="plaintext">Rv3327 S - Function unknown </span>
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2618
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2553
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<pre style="margin: 0;"> <span id="LC2553" class="line" lang="plaintext">Rv3327 L - Replication, recombination and repair </span>
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<pre style="margin: 0;">+<span id="LC2554" class="line" lang="plaintext">Rv3327 S - Function unknown </span>
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2619
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2555
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<pre style="margin: 0;"> <span id="LC2555" class="line" lang="plaintext">Rv3328c K sigJ Transcription </span>
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2620
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2556
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<pre style="margin: 0;"> <span id="LC2556" class="line" lang="plaintext">Rv3329 H - Coenzyme transport and metabolism </span>
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2621
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2557
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<pre style="margin: 0;"> <span id="LC2557" class="line" lang="plaintext">Rv3330 M dacB1 Cell wall/membrane/envelope biogenesis </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2646,8 +2582,8 @@ Rv3366 J spoU Translation, ribosomal structure and biogenesis</td>
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2646
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2582
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<pre style="margin: 0;"> <span id="LC2582" class="line" lang="plaintext">Rv3368c C - Energy production and conversion </span>
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2647
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2583
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<pre style="margin: 0;"> <span id="LC2583" class="line" lang="plaintext">Rv3369 H - Coenzyme transport and metabolism </span>
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2648
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2584
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<pre style="margin: 0;"> <span id="LC2584" class="line" lang="plaintext">Rv3370c L dnaE2 Replication, recombination and repair </span>
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2649
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<pre style="margin: 0;">-<span id="LC2649" class="line" lang="plaintext">Rv3372 R otsB2 General function prediction only </span>
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2650
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2585
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<pre style="margin: 0;"> <span id="LC2585" class="line" lang="plaintext">Rv3372 G otsB2 Carbohydrate transport and metabolism </span>
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2586
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<pre style="margin: 0;">+<span id="LC2586" class="line" lang="plaintext">Rv3372 R otsB2 General function prediction only </span>
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2651
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2587
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<pre style="margin: 0;"> <span id="LC2587" class="line" lang="plaintext">Rv3373 I echA18 Lipid transport and metabolism </span>
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2652
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2588
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<pre style="margin: 0;"> <span id="LC2588" class="line" lang="plaintext">Rv3374 I echA18.1 Lipid transport and metabolism </span>
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2653
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2589
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<pre style="margin: 0;"> <span id="LC2589" class="line" lang="plaintext">Rv3375 J amiD Translation, ribosomal structure and biogenesis </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2662,13 +2598,12 @@ Rv3386 L - Replication, recombination and repair</td>
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2662
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2598
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<pre style="margin: 0;"> <span id="LC2598" class="line" lang="plaintext">Rv3387 L - Replication, recombination and repair </span>
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2663
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2599
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<pre style="margin: 0;"> <span id="LC2599" class="line" lang="plaintext">Rv3389c I - Lipid transport and metabolism </span>
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2664
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2600
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<pre style="margin: 0;"> <span id="LC2600" class="line" lang="plaintext">Rv3390 G lpqD Carbohydrate transport and metabolism </span>
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2665
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<pre style="margin: 0;">-<span id="LC2665" class="line" lang="plaintext">Rv3391 R acrA1 General function prediction only </span>
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2666
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2601
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<pre style="margin: 0;"> <span id="LC2601" class="line" lang="plaintext">Rv3391 Q acrA1 Secondary metabolites biosynthesis, transport and catabolism </span>
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2602
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<pre style="margin: 0;">+<span id="LC2602" class="line" lang="plaintext">Rv3391 R acrA1 General function prediction only </span>
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2667
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2603
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<pre style="margin: 0;"> <span id="LC2603" class="line" lang="plaintext">Rv3392c M cmaA1 Cell wall/membrane/envelope biogenesis </span>
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2668
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2604
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<pre style="margin: 0;"> <span id="LC2604" class="line" lang="plaintext">Rv3393 F iunH Nucleotide transport and metabolism </span>
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2669
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2605
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<pre style="margin: 0;"> <span id="LC2605" class="line" lang="plaintext">Rv3394c L - Replication, recombination and repair </span>
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2670
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2606
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<pre style="margin: 0;"> <span id="LC2606" class="line" lang="plaintext">Rv3396c F guaA Nucleotide transport and metabolism </span>
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2671
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<pre style="margin: 0;">-<span id="LC2671" class="line" lang="plaintext">Rv3396c F guaA Nucleotide transport and metabolism </span>
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2672
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2607
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<pre style="margin: 0;"> <span id="LC2607" class="line" lang="plaintext">Rv3397c I phyA Lipid transport and metabolism </span>
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2673
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2608
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<pre style="margin: 0;"> <span id="LC2608" class="line" lang="plaintext">Rv3398c H idsA1 Coenzyme transport and metabolism </span>
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2674
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2609
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<pre style="margin: 0;"> <span id="LC2609" class="line" lang="plaintext">Rv3399 Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2698,8 +2633,8 @@ Rv3428c L - Replication, recombination and repair</td>
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2698
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2633
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<pre style="margin: 0;"> <span id="LC2633" class="line" lang="plaintext">Rv3430c L - Replication, recombination and repair </span>
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2699
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2634
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<pre style="margin: 0;"> <span id="LC2634" class="line" lang="plaintext">Rv3431c L - Replication, recombination and repair </span>
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2635
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<pre style="margin: 0;"> <span id="LC2635" class="line" lang="plaintext">Rv3432c E gadB Amino acid transport and metabolism </span>
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<pre style="margin: 0;">-<span id="LC2701" class="line" lang="plaintext">Rv3433c S - Function unknown </span>
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<pre style="margin: 0;"> <span id="LC2636" class="line" lang="plaintext">Rv3433c G - Carbohydrate transport and metabolism </span>
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<pre style="margin: 0;">+<span id="LC2637" class="line" lang="plaintext">Rv3433c S - Function unknown </span>
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2638
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<pre style="margin: 0;"> <span id="LC2638" class="line" lang="plaintext">Rv3436c M glmS Cell wall/membrane/envelope biogenesis </span>
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2639
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<pre style="margin: 0;"> <span id="LC2639" class="line" lang="plaintext">Rv3441c G mrsA Carbohydrate transport and metabolism </span>
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2640
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<pre style="margin: 0;"> <span id="LC2640" class="line" lang="plaintext">Rv3442c J rpsI Translation, ribosomal structure and biogenesis </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2901,8 +2836,6 @@ Rv3725 G - Carbohydrate transport and metabolism</td>
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2836
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<pre style="margin: 0;"> <span id="LC2836" class="line" lang="plaintext">Rv3726 R - General function prediction only </span>
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2837
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<pre style="margin: 0;"> <span id="LC2837" class="line" lang="plaintext">Rv3727 S - Function unknown </span>
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2838
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<pre style="margin: 0;"> <span id="LC2838" class="line" lang="plaintext">Rv3728 R - General function prediction only </span>
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<pre style="margin: 0;">-<span id="LC2904" class="line" lang="plaintext">Rv3728 R - General function prediction only </span>
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<pre style="margin: 0;">-<span id="LC2905" class="line" lang="plaintext">Rv3729 R - General function prediction only </span>
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2839
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<pre style="margin: 0;"> <span id="LC2839" class="line" lang="plaintext">Rv3729 R - General function prediction only </span>
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2840
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<pre style="margin: 0;"> <span id="LC2840" class="line" lang="plaintext">Rv3730c L - Replication, recombination and repair </span>
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2841
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<pre style="margin: 0;"> <span id="LC2841" class="line" lang="plaintext">Rv3731 L ligC Replication, recombination and repair </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2911,7 +2844,6 @@ Rv3733c R - General function prediction only</td>
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2911
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2844
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<pre style="margin: 0;"> <span id="LC2844" class="line" lang="plaintext">Rv3735 S - Function unknown </span>
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2912
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2845
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<pre style="margin: 0;"> <span id="LC2845" class="line" lang="plaintext">Rv3736 K - Transcription </span>
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2846
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<pre style="margin: 0;"> <span id="LC2846" class="line" lang="plaintext">Rv3737 S - Function unknown </span>
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<pre style="margin: 0;">-<span id="LC2914" class="line" lang="plaintext">Rv3737 S - Function unknown </span>
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2847
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<pre style="margin: 0;"> <span id="LC2847" class="line" lang="plaintext">Rv3741c P - Inorganic ion transport and metabolism </span>
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2848
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<pre style="margin: 0;"> <span id="LC2848" class="line" lang="plaintext">Rv3742c P - Inorganic ion transport and metabolism </span>
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2917
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2849
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<pre style="margin: 0;"> <span id="LC2849" class="line" lang="plaintext">Rv3743c P ctpJ Inorganic ion transport and metabolism </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2941,7 +2873,6 @@ Rv3782 R - General function prediction only</td>
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2941
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2873
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<pre style="margin: 0;"> <span id="LC2873" class="line" lang="plaintext">Rv3783 M rfbD Cell wall/membrane/envelope biogenesis </span>
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2942
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2874
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<pre style="margin: 0;"> <span id="LC2874" class="line" lang="plaintext">Rv3784 G - Carbohydrate transport and metabolism </span>
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2943
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2875
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<pre style="margin: 0;"> <span id="LC2875" class="line" lang="plaintext">Rv3786c M - Cell wall/membrane/envelope biogenesis </span>
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2944
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<pre style="margin: 0;">-<span id="LC2944" class="line" lang="plaintext">Rv3786c M - Cell wall/membrane/envelope biogenesis </span>
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2945
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2876
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<pre style="margin: 0;"> <span id="LC2876" class="line" lang="plaintext">Rv3787c Q - Secondary metabolites biosynthesis, transport and catabolism </span>
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2946
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2877
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<pre style="margin: 0;"> <span id="LC2877" class="line" lang="plaintext">Rv3788 K - Transcription </span>
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2947
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2878
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<pre style="margin: 0;"> <span id="LC2878" class="line" lang="plaintext">Rv3789 S - Function unknown </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2952" style="width: 35px; color: rgba(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="2883" style="width: 35px; color: rgba(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">@@ -2952,7 +2883,6 @@ Rv3797 I fadE35 Lipid transport and metabolism</td>
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2952
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2883
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<pre style="margin: 0;"> <span id="LC2883" class="line" lang="plaintext">Rv3798 L - Replication, recombination and repair </span>
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2953
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2884
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<pre style="margin: 0;"> <span id="LC2884" class="line" lang="plaintext">Rv3799c I accD4 Lipid transport and metabolism </span>
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2954
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2885
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<pre style="margin: 0;"> <span id="LC2885" class="line" lang="plaintext">Rv3800c Q pks13 Secondary metabolites biosynthesis, transport and catabolism </span>
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2955
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<pre style="margin: 0;">-<span id="LC2955" class="line" lang="plaintext">Rv3800c Q pks13 Secondary metabolites biosynthesis, transport and catabolism </span>
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2956
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2886
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<pre style="margin: 0;"> <span id="LC2886" class="line" lang="plaintext">Rv3801c Q fadD32 Secondary metabolites biosynthesis, transport and catabolism </span>
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2957
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2887
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<pre style="margin: 0;"> <span id="LC2887" class="line" lang="plaintext">Rv3803c R fbpD General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="2958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2958
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2888
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<pre style="margin: 0;"> <span id="LC2888" class="line" lang="plaintext">Rv3804c R fbpA General function prediction only </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2967" style="width: 35px; color: rgba(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="2897" style="width: 35px; color: rgba(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">@@ -2967,7 +2897,6 @@ Rv3815c I - Lipid transport and metabolism</td>
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2967
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2897
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<pre style="margin: 0;"> <span id="LC2897" class="line" lang="plaintext">Rv3816c I - Lipid transport and metabolism </span>
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2968
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2898
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<pre style="margin: 0;"> <span id="LC2898" class="line" lang="plaintext">Rv3817 J - Translation, ribosomal structure and biogenesis </span>
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2969
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2899
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<pre style="margin: 0;"> <span id="LC2899" class="line" lang="plaintext">Rv3818 R - General function prediction only </span>
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2970
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<pre style="margin: 0;">-<span id="LC2970" class="line" lang="plaintext">Rv3818 R - General function prediction only </span>
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2971
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2900
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<pre style="margin: 0;"> <span id="LC2900" class="line" lang="plaintext">Rv3820c Q papA2 Secondary metabolites biosynthesis, transport and catabolism </span>
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2972
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2901
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<pre style="margin: 0;"> <span id="LC2901" class="line" lang="plaintext">Rv3823c R mmpL8 General function prediction only </span>
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<td class="diff-line-num old_line" data-linenumber="2973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2973
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2902
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<pre style="margin: 0;"> <span id="LC2902" class="line" lang="plaintext">Rv3824c Q papA1 Secondary metabolites biosynthesis, transport and catabolism </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2994" style="width: 35px; color: rgba(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="2923" style="width: 35px; color: rgba(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">@@ -2994,8 +2923,6 @@ Rv3855 K ethR Transcription</td>
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2994
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2923
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<pre style="margin: 0;"> <span id="LC2923" class="line" lang="plaintext">Rv3856c R - General function prediction only </span>
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2995
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2924
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<pre style="margin: 0;"> <span id="LC2924" class="line" lang="plaintext">Rv3858c R gltD General function prediction only </span>
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2996
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2925
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<pre style="margin: 0;"> <span id="LC2925" class="line" lang="plaintext">Rv3859c E gltB Amino acid transport and metabolism </span>
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2997
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<pre style="margin: 0;">-<span id="LC2997" class="line" lang="plaintext">Rv3859c E gltB Amino acid transport and metabolism </span>
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2998
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<pre style="margin: 0;">-<span id="LC2998" class="line" lang="plaintext">Rv3859c E gltB Amino acid transport and metabolism </span>
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2999
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2926
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<pre style="margin: 0;"> <span id="LC2926" class="line" lang="plaintext">Rv3862c J whiB6 Translation, ribosomal structure and biogenesis </span>
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<td class="diff-line-num old_line" data-linenumber="3000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3000
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<td class="diff-line-num new_line" data-linenumber="2927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2927
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<pre style="margin: 0;"> <span id="LC2927" class="line" lang="plaintext">Rv3868 O - Posttranslational modification, protein turnover, chaperones </span>
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3001
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2928
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<pre style="margin: 0;"> <span id="LC2928" class="line" lang="plaintext">Rv3870 D - Cell cycle control, cell division, chromosome partitioning </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3006" style="width: 35px; color: rgba(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="2933" style="width: 35px; color: rgba(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">@@ -3006,7 +2933,6 @@ Rv3883c O mycP1 Posttranslational modification, protein turnover, chaperones</td>
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3006
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<td class="diff-line-num new_line" data-linenumber="2933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2933
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<pre style="margin: 0;"> <span id="LC2933" class="line" lang="plaintext">Rv3884c O - Posttranslational modification, protein turnover, chaperones </span>
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3007
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2934
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<pre style="margin: 0;"> <span id="LC2934" class="line" lang="plaintext">Rv3886c O mycP2 Posttranslational modification, protein turnover, chaperones </span>
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3008
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2935
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<pre style="margin: 0;"> <span id="LC2935" class="line" lang="plaintext">Rv3888c D - Cell cycle control, cell division, chromosome partitioning </span>
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3009
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<pre style="margin: 0;">-<span id="LC3009" class="line" lang="plaintext">Rv3888c D - Cell cycle control, cell division, chromosome partitioning </span>
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3010
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2936
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<pre style="margin: 0;"> <span id="LC2936" class="line" lang="plaintext">Rv3890c S esxC Function unknown </span>
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<td class="diff-line-num old_line" data-linenumber="3011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3011
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2937
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<pre style="margin: 0;"> <span id="LC2937" class="line" lang="plaintext">Rv3894c D - Cell cycle control, cell division, chromosome partitioning </span>
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3012
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2938
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<pre style="margin: 0;"> <span id="LC2938" class="line" lang="plaintext">Rv3896c R - General function prediction only </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3019" style="width: 35px; color: rgba(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="2945" style="width: 35px; color: rgba(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">@@ -3019,7 +2945,6 @@ Rv3911 K sigM Transcription</td>
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3019
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2945
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<pre style="margin: 0;"> <span id="LC2945" class="line" lang="plaintext">Rv3913 O trxB2 Posttranslational modification, protein turnover, chaperones </span>
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3020
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2946
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<pre style="margin: 0;"> <span id="LC2946" class="line" lang="plaintext">Rv3914 C trxC Energy production and conversion </span>
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<td class="diff-line-num old_line" data-linenumber="3021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3021
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2947
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<pre style="margin: 0;"> <span id="LC2947" class="line" lang="plaintext">Rv3915 M - Cell wall/membrane/envelope biogenesis </span>
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3022
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<pre style="margin: 0;">-<span id="LC3022" class="line" lang="plaintext">Rv3915 M - Cell wall/membrane/envelope biogenesis </span>
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3023
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2948
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<pre style="margin: 0;"> <span id="LC2948" class="line" lang="plaintext">Rv3917c K parB Transcription </span>
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<td class="diff-line-num old_line" data-linenumber="3024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3024
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2949
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<pre style="margin: 0;"> <span id="LC2949" class="line" lang="plaintext">Rv3918c D parA Cell cycle control, cell division, chromosome partitioning </span>
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3025
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2950
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<pre style="margin: 0;"> <span id="LC2950" class="line" lang="plaintext">Rv3919c M gidB Cell wall/membrane/envelope biogenesis </span>
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<li id="b09ef31d42e430ff42b72b80215384a2ddaf2f06">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#b09ef31d42e430ff42b72b80215384a2ddaf2f06"><strong>src/pytransit/data/H37Rv_sanger_roles.dat</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">@@ -321,40 +321,40 @@ Rv2994 III</td>
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321
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="plaintext">Rv3065 III.A.6</span>
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322
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="plaintext">Rv3065 III.A</span>
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323
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="plaintext">Rv3065 III</span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="plaintext">Rv0233 I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">Rv0233 I.F.3</span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="plaintext">Rv0233 I.F</span>
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="plaintext">Rv0233 I</span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="plaintext">Rv0321 I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">Rv0321 I.F.3</span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="plaintext">Rv0321 I.F</span>
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="plaintext">Rv0321 I</span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="plaintext">Rv0570 I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">Rv0570 I.F.3</span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="plaintext">Rv0570 I.F</span>
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="plaintext">Rv0570 I</span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext">Rv1981c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">Rv1981c I.F.3</span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext">Rv1981c I.F</span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="plaintext">Rv1981c I</span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="plaintext">Rv2697c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">Rv2697c I.F.3</span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="plaintext">Rv2697c I.F</span>
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="plaintext">Rv2697c I</span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="plaintext">Rv2764c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">Rv2764c I.F.3</span>
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="plaintext">Rv2764c I.F</span>
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="plaintext">Rv2764c I</span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="plaintext">Rv3048c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">Rv3048c I.F.3</span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext">Rv3048c I</span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext">Rv3051c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="plaintext">Rv3051c I</span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="plaintext">Rv3052c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="plaintext">Rv3052c I</span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="plaintext">Rv3053c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="plaintext">Rv3053c I.F</span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="plaintext">Rv3053c I</span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="plaintext">Rv3247c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext">Rv3247c I.F</span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext">Rv3247c I</span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="plaintext">Rv3752c I.F.3<span class="idiff left right"> 2'</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">Rv3752c I.F.3</span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext">Rv3752c I.F</span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="plaintext">Rv3752c I</span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="plaintext">Rv1121 I.B.5</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.. _`analysis_methods`:</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Analysis Methods</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">================</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">==================</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Analysis Methods</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">==================</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">TRANSIT has analysis methods capable of analyzing **Himar1** and **Tn5** datasets.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +14,7 @@ Below is a description of some of the methods.</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">.. _gumbel:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Gumbel</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">------</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"><span class="idiff left right">======</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">The Gumbel can be used to determine which genes are essential in a</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">single condition. It does a gene-by-gene analysis of the insertions at</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,7 +26,7 @@ probability of this using a Bayesian model.</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> Intended only for **Himar1** datasets.</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">How does it work?</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"><span class="idiff left right">-----------------</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">| For a formal description of how this method works, see our paper [DeJesus2013]_:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,7 +35,7 @@ How does it work?</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">| `Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. <http://www.ncbi.nlm.nih.gov/pubmed/23361328>`_ *Bioinformatics*, 29(6):695-703.</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Example</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,7 +53,7 @@ Example</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">Parameters</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">- **Samples:** Gumbel uses Metropolis-Hastings (MH) to generate samples</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> of posterior distributions. The default setting is to run the</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,7 +88,7 @@ Parameters</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">Outputs and diagnostics</span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"><span class="idiff left right">-----------------------</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">The Gumbel method generates a tab-separated output file at the location</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">chosen by the user. This file will automatically be loaded into the</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,7 +138,7 @@ defined as follows:</td>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">|</span>
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138
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>
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139
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">Run-time</span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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141
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"></span>
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142
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext">The Gumbel method takes on the order of 10 minutes for 10,000 samples.</span>
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143
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext">Run-time is linearly proportional to the 'samples' parameter, or length</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -151,7 +152,7 @@ replicates; replicate datasets will be automatically merged.</td>
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151
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"></span>
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152
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext">griffin</span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"><span class="idiff left right">=======</span></span>
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155
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"></span>
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156
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext">This is an earlier version of the Gumbel method that</span>
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157
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext">identifies essential genes based on how unlikely 'gaps'</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,7 +177,7 @@ of estimating internal parameters.</td>
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176
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext">.. _`tn5gaps`:</span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">Tn5Gaps</span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"><span class="idiff left right">=======</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext"></span>
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181
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">The Tn5Gaps method can be used to determine which genes are essential</span>
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182
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext">in a single condition for **Tn5** datasets. It does an analysis of the</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -193,7 +194,7 @@ the Gumbel distribution.</td>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="plaintext">|</span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext">How does it work?</span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"><span class="idiff left right">-----------------</span></span>
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197
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext">This method is loosely is based on the original gumbel analysis</span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext">method described in this paper:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="230" style="width: 35px; color: rgba(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">@@ -230,7 +231,7 @@ output of our analysis.</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="plaintext">Usage</span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext"><span class="idiff left right">~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"><span class="idiff left right">-----</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="plaintext"> python3 ../../../transit.py tn5gaps <comma-separated .wig files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -243,7 +244,7 @@ Usage</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext">Parameters</span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext">+ **Minimum Read:** The minimum read count that is considered a true read. Because the Gumbel method depends on determining gaps of TA sites lacking insertions, it may be suceptible to spurious reads (e.g. errors). The default value of 1 will consider all reads as true reads. A value of 2, for example, will ignore read counts of 1.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -256,7 +257,7 @@ Parameters</td>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext">+ **-iC:** Trimming of insertions in C-terminus (given as percentage of ORF length, e.g. "5" for 5%; default=0)</span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext">Example</span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"> python3 PATH/src/transit.py tn5gaps salmonella_baseline.wig Salmonella-Ty2.prot_table salmonella_baseline_tn5gaps_trimmed.dat -m 2 -r Sum -iN 5 -iC 5</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -267,7 +268,7 @@ These input and output files can be downloaded from the **Example Data** section</td>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext">Outputs and diagnostics</span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"><span class="idiff left right">-----------------------</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="plaintext">The Tn5Gaps method generates a tab-separated output file at the</span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext">location chosen by the user. This file will automatically be loaded</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -306,7 +307,7 @@ file are defined as follows:</td>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="plaintext">Run-time</span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="plaintext">The Tn5Gaps method takes on the order of 10 minutes.</span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="plaintext">Other notes: Tn5Gaps can be run on multiple replicates; replicate</span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="plaintext">datasets will be automatically merged.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,7 +322,7 @@ datasets will be automatically merged.</td>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="plaintext">.. _HMM:</span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="plaintext">HMM</span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="plaintext"><span class="idiff left right">---</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"><span class="idiff left right">===</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="plaintext">The HMM method can be used to determine the essentiality of the entire genome, as opposed to gene-level analysis of the other methods. It is capable of identifying regions that have unusually high or unusually low read counts (i.e. growth advantage or growth defect regions), in addition to the more common categories of essential and non-essential.</span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -331,7 +332,7 @@ The HMM method can be used to determine the essentiality of the entire genome, a</td>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext">How does it work?</span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"><span class="idiff left right">-----------------</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="plaintext">| For a formal description of how this method works, see our paper [DeJesus2013HMM]_:</span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="plaintext">|</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -341,7 +342,7 @@ How does it work?</td>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext">Example</span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -355,7 +356,7 @@ Example</td>
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext">Parameters</span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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359
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360
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="plaintext">The HMM method automatically estimates the necessary statistical</span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="plaintext">parameters from the datasets. You can change how the method handles</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -370,7 +371,7 @@ replicate datasets:</td>
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370
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="plaintext">Output and Diagnostics</span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext"><span class="idiff left right">----------------------</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="plaintext">| The HMM method outputs two files. The first file provides the most</span>
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376
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="plaintext"> likely assignment of states for all the TA sites in the genome. Sites</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -441,7 +442,7 @@ Output and Diagnostics</td>
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441
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442
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="plaintext">|</span>
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="plaintext"></span>
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443
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="plaintext">Run-time</span>
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444
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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446
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="plaintext">| The HMM method takes less than 10 minutes to complete. The parameters</span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="plaintext"> of the method should not affect the running-time.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -455,7 +456,7 @@ Run-time</td>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="plaintext">.. _resampling:</span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="plaintext">Resampling</span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"><span class="idiff left right">==========</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="plaintext">The resampling method is a comparative analysis the allows that can be</span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="plaintext">used to determine conditional essentiality of genes. It is based on a</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -474,7 +475,7 @@ of genes or known biological pathway.</td>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="plaintext">How does it work?</span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"><span class="idiff left right">-----------------</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="plaintext">This technique has yet to be formally published in the context of</span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="plaintext">differential essentiality analysis. Briefly, the read-counts at each</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -490,7 +491,7 @@ original, observed difference in read-counts.</td>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="plaintext">Usage</span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="plaintext"><span class="idiff left right">~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext"><span class="idiff left right">-----</span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="plaintext">::</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -518,7 +519,7 @@ Usage</td>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="plaintext"></span>
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="plaintext"></span>
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="plaintext">Parameters</span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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522
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523
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="plaintext"></span>
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523
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="plaintext">The resampling method is non-parametric, and therefore does not require</span>
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524
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="plaintext">any parameters governing the distributions or the model. The following</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -575,7 +576,7 @@ parameters are available for the method:</td>
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575
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="plaintext">|</span>
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576
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="plaintext"></span>
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577
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="plaintext">Notes</span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="plaintext"><span class="idiff left right">~~~~~</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext"><span class="idiff left right">-----</span></span>
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579
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="plaintext"></span>
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580
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="plaintext">I recommend using -a (adaptive resampling). It runs much faster, and the p-values</span>
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581
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="plaintext">will be very close to a full non-adaptive run (all 10,000 samples).</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -588,7 +589,7 @@ making it difficult to make confident calls on essentiality.</td>
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588
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="plaintext"></span>
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589
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="plaintext"></span>
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590
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="plaintext">Doing resampling with a combined_wig file</span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext"><span class="idiff left right">-----------------------------------------</span></span>
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592
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="plaintext"></span>
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593
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="plaintext">Resampling can also now take a combined_wig_ file as input (containing insertion counts</span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="plaintext">for multiple sample), along with a samples_metadata_ file</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -608,7 +609,7 @@ If you want to compare more than two conditions, see :ref:`ZINB <zinb>`.</td>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="plaintext"></span>
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="plaintext"></span>
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="plaintext">Doing resampling with datasets from different libraries.</span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext"><span class="idiff left right">--------------------------------------------------------</span></span>
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="plaintext"></span>
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="plaintext">In most cases, comparisons are done among samples (replicates) from</span>
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614
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="plaintext">the same library evaluated in two different conditions. But if the</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -626,7 +627,7 @@ from each library in each condition.</td>
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="plaintext"></span>
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="plaintext"></span>
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628
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="plaintext">Doing resampling between different strains.</span>
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629
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext"><span class="idiff left right">-------------------------------------------</span></span>
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630
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631
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="plaintext"></span>
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="plaintext">The most common case is that resampling is done among replicates all</span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="plaintext">from the same Tn library, and hence all the datasets (fastq files) are</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -698,7 +699,7 @@ replicates in condition B will be from another library (another strain).</td>
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698
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="plaintext">|</span>
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700
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="plaintext"></span>
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701
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="plaintext">Output and Diagnostics</span>
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701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="plaintext"><span class="idiff left right">----------------------</span></span>
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="plaintext">The resampling method outputs a tab-delimited file with results for each</span>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="plaintext">gene in the genome. P-values are adjusted for multiple comparisons using</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -752,7 +753,7 @@ changed using the -PC flag (above).</td>
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="plaintext">|</span>
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="plaintext"></span>
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754
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="plaintext">Run-time</span>
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755
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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756
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="plaintext"></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="plaintext">A typical run of the resampling method with 10,000 samples will take</span>
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758
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="plaintext">around 45 minutes (with the histogram option ON). Using the *adaptive</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -764,7 +765,7 @@ resampling* option (-a), the run-time is reduced to around 10 minutes.</td>
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764
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="plaintext">----</span>
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="plaintext"></span>
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766
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="plaintext">Mann-Whitney U-test (utest)</span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="plaintext"><span class="idiff left right">---------------------------</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="plaintext"><span class="idiff left right">===========================</span></span>
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="plaintext"></span>
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769
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="plaintext">This is a method for comparing datasets from a TnSeq library evaluated in</span>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="plaintext">two different conditions, analogous to resampling.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -788,13 +789,13 @@ A reference for this method is `(Santa Maria et al., 2014)</td>
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788
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="plaintext">.. _genetic-interactions:</span>
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789
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="plaintext"></span>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="plaintext">Genetic Interactions</span>
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791
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="plaintext"><span class="idiff left right">--------------------</span></span>
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext"><span class="idiff left right">====================</span></span>
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="plaintext"></span>
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="plaintext">The genetic interactions (GI) method is a comparative analysis used</span>
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="plaintext">used to determine genetic interactions. It is a Bayesian method</span>
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="plaintext">that estimates the distribution of log fold-changes (logFC) in two</span>
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796
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="plaintext">strain backgrounds under different conditions, and identifies significantly</span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="plaintext">large changes in enrichment (delta<span class="idiff left right">-</span>logFC) to identify those genes</span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="plaintext">large changes in enrichment (delta<span class="idiff left right">_</span>logFC) to identify those genes</span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="plaintext">that imply a genetic interaction.</span>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="plaintext"></span>
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -805,7 +806,7 @@ that imply a genetic interaction.</td>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="plaintext">|</span>
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="plaintext"></span>
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="plaintext">How does it work?</span>
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="plaintext"><span class="idiff left right">-----------------</span></span>
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="plaintext">GI performs a comparison among 4 groups of datasets, strain A and B assessed in conditions 1 and 2 (e.g. control vs treatment).</span>
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="plaintext">It looks for interactions where the response to the treatment (i.e. effect on insertion counts) depends on the strain.</span>
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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">@@ -825,28 +826,92 @@ slopes between strain A and B (represented by 'delta_LFC' in the output file).</td>
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="plaintext">|</span>
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="plaintext"></span>
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="plaintext">Statistical Significance</span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="plaintext">------------------------</span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="plaintext"></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="plaintext">The computation that is done by GI is to compute the posterior distribution of the delta_LFC (or mean change in slopes)</span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="plaintext">through Bayesian sampling.</span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="plaintext">The primary method to determine significance of genes is whethter this the mean_delta_LFC is significantly differnt than 0.</span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="plaintext">However, since the mean_delta_LFC is a distribution, we represent it by a Highest Density Interval, HDI, which is </span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="plaintext">similar to a 95% confidence interval. Furthermore, rather than asking whether the HDI overlaps 0 exactly, we expand the interval</span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="plaintext">around 0 to a Region of Probable Equivalence (ROPE), which is set to [-0.5,0.5] by default. Hence the significant genes</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="plaintext">are those for which the HDI does not overlap the ROPE. GI has a flag to adjust the size of the ROPE, if desired.</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="plaintext">In the GI output file, the final column give the significance call, along with type of interaction.</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="plaintext">If a gene is not significant, it will be marked with "**No Interaction**" (for the HDI method, meaning HDI overlaps the ROPE).</span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="plaintext">If a gene IS significant, then its interaction will be cateogrized in 3 types (see NAR paper):</span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="plaintext"></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="plaintext"> * **Aggravating** - mean_delta_LFC is negative; gene is more required in treatment than control in the B strain, compared to the A strain</span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="plaintext"> * **Suppressive** - mean_delta_LFC is positive, and the gene was not conditionally essential in strain A (flat slope), but becomes conditionally non-essential in strain B when treated (positive slope)</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="plaintext"> * **Alleviating** - mean_delta_LFC is positive, but the conditional requirement (negative slope) of the gene in strain A with treatment is "cancelled" by the modification in strain B</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="plaintext"></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="plaintext">.. image:: _images/genetic_interaction_types.png</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="plaintext"></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="plaintext">A limitation of this HDI approach is that it is discrete (i.e. overlap is either True or False), but does not provide a quantitative metric</span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="plaintext">for the degree of overlap. Thus a second method for assessing significance of genetic interactions is to compute</span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="plaintext">the probability of overlap. The lower the probability, the more differnt the delta_LFC is from 0, indicating a more</span>
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="plaintext">significant interaction. In this case, genes with prob < 0.05 are considered interactions and classified by the 3 types above,</span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="plaintext">while genes with prob >= 0.05 are marked as "No Interaction".</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="plaintext"></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="plaintext">In addition, since we are calculating significance for thousands of genes in parallel, </span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="plaintext">many researchers prefer to have some method for correcting for multiple tests, to control the false discovery rate.</span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="plaintext">However, FDR correction is generally used only for frequentist analyses, and he GI method is fundamentally a Bayesian approach.</span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="plaintext">Technically, in a Bayesian framework, FDR correction is not needed. Any adjustment for expectations about number of hits</span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="plaintext">would be achieved through adjusting parameters for prior distributions. Nonetheless, GI includes options for </span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="plaintext">two methods that approximate FDR correction: **BFDR** (Bayesian False Discovery Rate correction,</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="plaintext">`Newton M.A., Noueiry A., Sarkar D., Ahlquist P. (2004). Detecting differential gene expression with a semiparametric hierarchical </span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="plaintext">mixture method. Biostatistics, 5:155–176. <https://pubmed.ncbi.nlm.nih.gov/15054023/>`_) and FWER (Familty-Wise</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="plaintext">Error Rate control). When these corrections are applied, a threshold of 0.05 for the adjusted probability of overlap </span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="plaintext">is used for each, and this determines which</span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="plaintext">genes are classified as interacting (1 of 3 types) or marked as "No Interaction", as above.</span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="plaintext"></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="plaintext">In order to enable users to evaluate these various methods for determining significance of interactions,</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="plaintext">a '-signif' flag is provided for the GI method. The options are:</span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="plaintext"> * **-signif HDI**: significant genes are those for which the HDI does not overlap the ROPE</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="plaintext"> * **-signif prob**: significant genes are those with prob < 0.05, where 'prob' is porbability that HDI overlap the ROPE (default)</span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="plaintext"> * **-signif BFDR**: significant genes are those with adjusted prob < 0.05, where prob is adjusted by the BFDR method</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="plaintext"> * **-signif FWER**: significant genes are those with adjusted prob < 0.05, where prob is adjusted by the FWER method</span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="plaintext"></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="plaintext">'-signif prob' is the default method.</span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="plaintext"></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="plaintext">In the output file, the genes are sorted by the probability that the HDI overlaps the ROPE.</span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="plaintext">The genes at the top are rougly the genes with the highest absolute value of mean_delta_LFC.</span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="plaintext"></span>
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882
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828
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="plaintext">Usage</span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="plaintext"><span class="idiff left right">~~~~~</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="plaintext"><span class="idiff left right">-----</span></span>
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830
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="plaintext"></span>
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831
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="plaintext">::</span>
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832
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="plaintext"></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="plaintext"> python3 transit.py GI <wigs_for_strA_cond1> <wigs_for_strA_cond2> <wigs_for_strB_cond1> <wigs_for_strB_cond2> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="plaintext"> python3 <span class="idiff left right">/pacific/home/ioerger/transit/src/</span>transit.py GI <wigs_for_strA_cond1> <wigs_for_strA_cond2> <wigs_for_strB_cond1> <wigs_for_strB_cond2> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span>
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834
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="plaintext"></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="plaintext"> GI performs a comparison among 4 groups of datasets, strain A and B assessed in conditions 1 and 2 (e.g. control vs treatment).</span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="plaintext"> It looks for interactions where the response to the treatment (i.e. effect on insertion counts) depends on the strain (output variable: delta_LFC).</span>
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835
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892
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="plaintext"> Provide replicates in each group as a comma-separated list of wig files.</span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="plaintext"> HDI is highest density interval for posterior distribution of delta_LFC, which is like a confidence interval on difference of slopes.</span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="plaintext"> Genes are sorted by probability of HDI overlapping with ROPE. (genes with the highest abs(mean_delta_logFC) are near the top, approximately)</span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="plaintext"> Significant genes are indicated by 'Type of Interaction' column (No Interaction, Aggravating, Alleviating, Suppressive).</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="plaintext"> By default, hits are defined as "Is HDI outside of ROPE?"=TRUE (i.e. non-overlap of delta_LFC posterior distritbuion with Region of Probably Equivalence around 0)</span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="plaintext"> Alternative methods for significance: use -signif flag with prob, BFDR, or FWER. These affect 'Type of Interaction' (i.e. which genes are labeled 'No Interaction')</span>
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836
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="plaintext"></span>
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837
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="plaintext"> Optional Arguments:</span>
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838
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="plaintext"> -s <integer> := Number of samples. Default: -s 10000</span>
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839
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="plaintext"> --rope <float> := Region of Practical Equivalence. Area around 0 (i.e. 0 +/- ROPE) that is NOT of interest. Can be thought of similar to the area of the null-hypothesis. Default: --rope 0.5</span>
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840
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="plaintext"> -n <string> := Normalization method. Default: -n TTR</span>
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841
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="plaintext"> -iz := Include rows with zero ac<span class="idiff left right">c</span>ross conditions.</span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="plaintext"> -iz := Include rows with zero across conditions.</span>
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842
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904
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<pre style="margin: 0;"> <span id="LC904" class="line" lang="plaintext"> -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Turned Off.</span>
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843
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905
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="plaintext"> -iN <float> := Ignore TAs occuring at given percentage (as integer) of the N terminus. Default: -iN 0</span>
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="plaintext"> -iC <float> := Ignore TAs occuring at given percentage (as integer) of the C terminus. Default: -iC 0</span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="plaintext"> -signif HDI := (default) Significant if HDI does not overlap ROPE; if HDI overlaps ROPE, 'Type of Interaction' is set to 'No Interaction'</span>
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="plaintext"> -signif prob := Optionally, significant hits are re-defined based on probability (degree) of overlap of HDI with ROPE, prob<0.05 (no adjustment)</span>
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="plaintext"> -signif BFDR := Apply "Bayesian" FDR correction (see doc) to adjust HDI-ROPE overlap probabilities so that significant hits are re-defined as BFDR<0.05</span>
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="plaintext"> -signif FWER := Apply "Bayesian" FWER correction (see doc) to adjust HDI-ROPE overlap probabilities so that significant hits are re-defined as FWER<0.05</span>
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="plaintext">You can think of 'control' and 'experimental' samples as 'untreated' vs. 'treated'.</span>
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="plaintext"></span>
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848
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913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="plaintext">Example</span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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850
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915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="plaintext"></span>
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916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="plaintext">In this example, the effect of a knockout of SigB is being evaluated for its effect on tolerance of isoniazid.</span>
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852
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917
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="plaintext">Some genes may become more essential (or less) in the presence of INH in the wild-type strain.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -859,7 +924,7 @@ Note there are 2 replicates in each of the 4 groups of datasets.</td>
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="plaintext"></span>
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="plaintext"></span>
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861
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926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="plaintext">Parameters</span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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863
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="plaintext"></span>
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864
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="plaintext">The resampling method is non-parametric, and therefore does not require</span>
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865
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="plaintext">any parameters governing the distributions or the model. The following</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -890,17 +955,23 @@ parameters are available for the method:</td>
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890
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955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="plaintext"> as real differences. See the :ref:`Normalization <normalization>` section for a description</span>
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891
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="plaintext"> of normalization method available in TRANSIT.</span>
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="plaintext">- **Significance Method:**</span>
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="plaintext"> * -signif HDI: significant genes are those for which the HDI does not overlap the ROPE</span>
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="plaintext"> * -signif prob: significant genes are those with prob < 0.05, where 'prob' is porbability that HDI overlap the ROPE (default)</span>
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="plaintext"> * -signif BFDR: significant genes are those with adjusted prob < 0.05, where prob is adjusted by the BFDR method</span>
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="plaintext"> * -signif FWER: significant genes are those with adjusted prob < 0.05, where prob is adjusted by the FWER method</span>
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966
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="plaintext">Output and Diagnostics</span>
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898
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~</span></span>
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="plaintext"><span class="idiff left right">----------------------</span></span>
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969
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="plaintext">The GI method outputs a tab-delimited file with results for each</span>
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901
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="plaintext">gene in the genome. P-values are adjusted for multiple comparisons using</span>
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902
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="plaintext">the Benjamini-Hochberg procedure (called "q-values" or "p-adj."). A</span>
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903
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="plaintext">typical threshold for conditional essentiality on is q-value < 0.05.</span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="plaintext">gene in the genome.</span>
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="plaintext">All genes are sorted by significance using the probability that the HDI overlaps the ROPE.</span>
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="plaintext">Significant genes are those NOT marked with 'No Interaction' in the last column.</span>
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="plaintext">+-----------------------------------------+----------------------------------------------------+</span>
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977
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="plaintext">| Column Header | Column Definition |</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -940,10 +1011,6 @@ typical threshold for conditional essentiality on is q-value < 0.05.</td>
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="plaintext"></span>
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941
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="plaintext">|</span>
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942
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="plaintext"></span>
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943
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="plaintext">Significant interactions are those with "HDI outside ROPE?"=TRUE.</span>
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944
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="plaintext"></span>
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945
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="plaintext">All genes are sorted by significance using BFDR.</span>
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946
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="plaintext"></span>
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947
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="plaintext"></span>
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948
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="plaintext"></span>
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949
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="plaintext">.. rst-class:: transit_sectionend</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -954,7 +1021,7 @@ All genes are sorted by significance using BFDR.</td>
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954
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1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="plaintext">.. _anova:</span>
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955
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1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="plaintext"></span>
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956
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="plaintext">ANOVA</span>
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957
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="plaintext"><span class="idiff left right">-----</span></span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="plaintext"><span class="idiff left right">=====</span></span>
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958
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="plaintext"></span>
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959
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1026
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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="plaintext">The Anova (Analysis of variance) method is used to determine which genes</span>
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960
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1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="plaintext">exhibit statistically significant variability of insertion counts across multiple conditions.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="966" style="width: 35px; color: rgba(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="1033" style="width: 35px; color: rgba(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">@@ -966,7 +1033,7 @@ to which experimental conditions).</td>
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966
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1033
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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="plaintext">|</span>
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967
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1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="plaintext"></span>
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968
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1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="plaintext">How does it work?</span>
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969
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~</span></span>
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1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="plaintext"><span class="idiff left right">-----------------</span></span>
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970
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="plaintext"></span>
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971
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="plaintext">The method performs the `One-way anova test <https://en.wikipedia.org/wiki/Analysis_of_variance?oldformat=true#The_F-test>`_ for each gene across conditions.</span>
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972
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="plaintext">It takes into account variability of normalized transposon insertion counts among TA sites</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1042" style="width: 35px; color: rgba(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">@@ -975,7 +1042,7 @@ to determine if the differences among the mean counts for each condition are sig</td>
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975
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="plaintext"></span>
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976
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
977
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<td class="diff-line-num new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="plaintext">Example</span>
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<td class="diff-line-num old old_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
978
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<td class="diff-line-num new_line old" data-linenumber="1045" style="width: 35px; color: rgba(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="LC978" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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<td class="diff-line-num new old_line" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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979
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
980
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<td class="diff-line-num new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="plaintext">::</span>
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<td class="diff-line-num old_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
981
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1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1014,7 +1081,7 @@ The filenames should match what is shown in the header of the combined_wig (incl</td>
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1014
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1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="plaintext"></span>
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1015
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1082
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1016
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1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="plaintext">Parameters</span>
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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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1018
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="plaintext"></span>
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1019
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1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="plaintext">The following parameters are available for the method:</span>
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<td class="diff-line-num old_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1020
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1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1030,7 +1097,7 @@ The following parameters are available for the method:</td>
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1030
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<td class="diff-line-num new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="plaintext">- **-PC** Pseudocounts to use in calculating LFCs (see below). Default: -PC 5</span>
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1031
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<td class="diff-line-num new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1032
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<td class="diff-line-num new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="plaintext">Output and Diagnostics</span>
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<td class="diff-line-num old old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="plaintext"><span class="idiff left right">----------------------</span></span>
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1034
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1101
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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="plaintext"></span>
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1035
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<td class="diff-line-num new_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="plaintext">The anova method outputs a tab-delimited file with results for each</span>
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1036
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1103
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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="plaintext">gene in the genome. P-values are adjusted for multiple comparisons using</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1144" style="width: 35px; color: rgba(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">@@ -1077,7 +1144,7 @@ Changing the pseudocounts will not affect the analysis of statistical significan</td>
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1077
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="plaintext">|</span>
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1078
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1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1079
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<td class="diff-line-num new_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="plaintext">Run-time</span>
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<td class="diff-line-num old old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1080
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<td class="diff-line-num new_line old" data-linenumber="1147" style="width: 35px; color: rgba(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="LC1080" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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<td class="diff-line-num old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1081
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<td class="diff-line-num new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1082
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<td class="diff-line-num new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="plaintext">A typical run of the anova method takes less than 1 minute for a combined wig file with 6 conditions, 3 replicates per condition.</span>
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<td class="diff-line-num old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1083
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<td class="diff-line-num new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1159" style="width: 35px; color: rgba(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">@@ -1092,7 +1159,7 @@ A typical run of the anova method takes less than 1 minute for a combined wig fi</td>
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<td class="diff-line-num old_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1092
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1159
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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="plaintext">.. _zinb:</span>
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<td class="diff-line-num old_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1093
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1160
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1094
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<td class="diff-line-num new_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="plaintext">ZINB</span>
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<td class="diff-line-num old old_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1095
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<td class="diff-line-num new_line old" data-linenumber="1162" style="width: 35px; color: rgba(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="LC1095" class="line" lang="plaintext"><span class="idiff left right">----</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="plaintext"><span class="idiff left right">====</span></span>
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<td class="diff-line-num old_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1096
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<td class="diff-line-num new_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1163
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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1097
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<td class="diff-line-num new_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="plaintext">The ZINB (Zero-Inflated Negative Binomial) method is used to determine</span>
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1098
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<td class="diff-line-num new_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="plaintext">which genes exhibit statistically significant variability in either</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1118" style="width: 35px; color: rgba(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="1185" style="width: 35px; color: rgba(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">@@ -1118,7 +1185,7 @@ See :ref:`Installation Instructions <install-zinb>`.</td>
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1118
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="plaintext">|</span>
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<td class="diff-line-num old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1119
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1120
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<td class="diff-line-num new_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1187
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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="plaintext">How does it work?</span>
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<td class="diff-line-num old old_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1121
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<td class="diff-line-num new_line old" data-linenumber="1188" style="width: 35px; color: rgba(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="LC1121" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~</span></span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="plaintext"><span class="idiff left right">-----------------</span></span>
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1122
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1189
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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="plaintext"></span>
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1123
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1190
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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="plaintext">| For a formal description of how this method works, see our paper [ZINB]_: </span>
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1124
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1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="plaintext">|</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1127" style="width: 35px; color: rgba(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="1194" style="width: 35px; color: rgba(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">@@ -1127,7 +1194,7 @@ How does it work?</td>
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1127
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1194
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<pre style="margin: 0;"> <span id="LC1194" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1128
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1195
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<pre style="margin: 0;"> <span id="LC1195" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1129
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<td class="diff-line-num new_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1196
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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="plaintext">Example</span>
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<td class="diff-line-num old old_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1130
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<td class="diff-line-num new_line old" data-linenumber="1197" style="width: 35px; color: rgba(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="LC1130" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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<td class="diff-line-num old_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1131
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1132
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1199
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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="plaintext">::</span>
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<td class="diff-line-num old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1133
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1200
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1149" style="width: 35px; color: rgba(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="1216" style="width: 35px; color: rgba(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">@@ -1149,7 +1216,7 @@ Example</td>
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1149
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1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="plaintext">.. _combined_wig:</span>
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1150
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1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1151
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1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="plaintext">Combined wig files</span>
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<td class="diff-line-num old old_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1152
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<td class="diff-line-num new_line old" data-linenumber="1219" style="width: 35px; color: rgba(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="LC1152" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="plaintext"><span class="idiff left right">------------------</span></span>
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1153
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1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="plaintext"></span>
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1154
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<td class="diff-line-num new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="plaintext">Transit now supports a new file format called 'combined_wig' which basically</span>
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1155
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<td class="diff-line-num new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="plaintext">combines multiple wig files into one file (with multiple columns). This is</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1174" style="width: 35px; color: rgba(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="1241" style="width: 35px; color: rgba(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">@@ -1174,7 +1241,7 @@ TTR is the default, but other relevant normalization options would be 'nonorm'</td>
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1174
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="plaintext">.. _samples_metadata:</span>
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1175
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="plaintext"></span>
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1176
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<td class="diff-line-num new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1243
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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="plaintext">Samples Metadata File</span>
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<td class="diff-line-num old old_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1177
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<td class="diff-line-num new_line old" data-linenumber="1244" style="width: 35px; color: rgba(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="LC1177" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~</span></span>
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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="plaintext"><span class="idiff left right">---------------------</span></span>
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1178
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="plaintext"></span>
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1179
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1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="plaintext">Format of the *samples_metadata* file: a tab-separated file (which you</span>
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1180
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1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="plaintext">can edit in Excel) with 3 columns: Id, Condition, and Filename (it</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1194" style="width: 35px; color: rgba(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="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1194,7 +1261,7 @@ of the combined_wig (including pathnames, if present).</td>
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1194
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1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="plaintext"> chol2 cholesterol /Users/example_data/cholesterol_rep3.wig</span>
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1195
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1262
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1196
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<td class="diff-line-num new_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1263
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<pre style="margin: 0;"> <span id="LC1263" class="line" lang="plaintext">Parameters</span>
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1197
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<pre style="margin: 0;">-<span id="LC1197" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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1198
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1265
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<pre style="margin: 0;"> <span id="LC1265" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1199
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<td class="diff-line-num new_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="plaintext">The following parameters are available for the method:</span>
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1200
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1208" style="width: 35px; color: rgba(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="1275" style="width: 35px; color: rgba(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">@@ -1208,7 +1275,7 @@ The following parameters are available for the method:</td>
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1208
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1275
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="plaintext">- **Covariates:** If additional covariates distinguishing the samples are available, such as library, timepoint, or genotype, they may be incorporated in the test.</span>
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1209
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1276
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1210
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="plaintext">Covariates and Interactions</span>
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<td class="diff-line-num old old_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1211
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<td class="diff-line-num new_line old" data-linenumber="1278" style="width: 35px; color: rgba(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="LC1211" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="plaintext"><span class="idiff left right">---------------------------</span></span>
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<td class="diff-line-num old_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="plaintext">While ZINB is focus on identifying variability of insertion counts across conditions,</span>
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1214
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="plaintext">the linear model also allows you to take other variables into account.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1281" style="width: 35px; color: rgba(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="1348" style="width: 35px; color: rgba(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">@@ -1281,7 +1348,7 @@ The difference between how covariates and interactions are handeled in the model</td>
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1281
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1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="plaintext">is discussed below in the section on Statistical Significance. </span>
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1282
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<td class="diff-line-num new_line" data-linenumber="1349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1349
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<pre style="margin: 0;"> <span id="LC1349" class="line" lang="plaintext"></span>
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1283
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<td class="diff-line-num new_line" data-linenumber="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1350
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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="plaintext">Categorical vs Numeric Covariates</span>
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<td class="diff-line-num old old_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1284
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<td class="diff-line-num new_line old" data-linenumber="1351" style="width: 35px; color: rgba(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="LC1284" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="plaintext"><span class="idiff left right">---------------------------------</span></span>
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1285
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1286
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<td class="diff-line-num new_line" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="plaintext">In some cases, covariates are intended to be treated as categorical</span>
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1287
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1354
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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="plaintext">variables, like 'batch' or 'library' or 'medium'.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1364" style="width: 35px; color: rgba(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">@@ -1297,7 +1364,7 @@ trend in the insertion counts as the covariate value increases.</td>
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1297
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1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="plaintext"></span>
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1298
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1365
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<pre style="margin: 0;"> <span id="LC1365" class="line" lang="plaintext"></span>
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1299
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1366
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<pre style="margin: 0;"> <span id="LC1366" class="line" lang="plaintext">Statistical Significance - What the P-values Mean in the ZINB Output</span>
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1300
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<td class="diff-line-num new_line old" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="plaintext"><span class="idiff left right">--------------------------------------------------------------------</span></span>
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1301
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1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1302
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<td class="diff-line-num new_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1369
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="plaintext">Formally, the P-value is from a likelihood ratio test (LRT) between a</span>
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<td class="diff-line-num old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="plaintext">condition-dependent ZINB model (:math:`m_1`) and a</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1391" style="width: 35px; color: rgba(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="1458" style="width: 35px; color: rgba(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">@@ -1391,7 +1458,7 @@ and this would be compared to the following null model (without the interaction</td>
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1391
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1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1392
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1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1393
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1460
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<pre style="margin: 0;"> <span id="LC1460" class="line" lang="plaintext">Output and Diagnostics</span>
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<td class="diff-line-num old old_line" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1394
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<td class="diff-line-num new_line old" data-linenumber="1461" style="width: 35px; color: rgba(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="LC1394" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~</span></span>
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1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="plaintext"><span class="idiff left right">----------------------</span></span>
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1395
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1462
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<pre style="margin: 0;"> <span id="LC1462" class="line" lang="plaintext"></span>
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1396
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1463
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<pre style="margin: 0;"> <span id="LC1463" class="line" lang="plaintext">The ZINB method outputs a tab-delimited file with results for each</span>
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1397
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1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="plaintext">gene in the genome. P-values are adjusted for multiple comparisons using</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1442" style="width: 35px; color: rgba(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="1509" style="width: 35px; color: rgba(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">@@ -1442,7 +1509,7 @@ Changing the pseudocounts will not affect the analysis of statistical significan</td>
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1442
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1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="plaintext">|</span>
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1443
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1510
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<pre style="margin: 0;"> <span id="LC1510" class="line" lang="plaintext"></span>
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1444
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1511
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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="plaintext">Run-time</span>
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1445
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<pre style="margin: 0;">-<span id="LC1445" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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<td class="diff-line-num old_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1446
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1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1447
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<td class="diff-line-num new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="plaintext">A typical run of the ZINB method takes ~5 minutes to analze a combined wig</span>
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<td class="diff-line-num old_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1448
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<td class="diff-line-num new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="plaintext">file with 6 conditions, 3 replicates per condition. It will, of</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1457" style="width: 35px; color: rgba(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="1524" style="width: 35px; color: rgba(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">@@ -1457,7 +1524,7 @@ course, run more slowly if you have many more conditions.</td>
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1457
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<td class="diff-line-num new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="plaintext">.. _normalization:</span>
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<td class="diff-line-num old_line" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1458
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<td class="diff-line-num new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<pre style="margin: 0;"> <span id="LC1525" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1459
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<td class="diff-line-num new_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="plaintext">Normalization</span>
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1460
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<td class="diff-line-num new_line old" data-linenumber="1527" style="width: 35px; color: rgba(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="LC1460" class="line" lang="plaintext"><span class="idiff left right">-------------</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1461" style="width: 35px; color: rgba(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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1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="plaintext"><span class="idiff left right">=============</span></span>
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<td class="diff-line-num old_line" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1461
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1528
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<pre style="margin: 0;"> <span id="LC1528" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1462
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<td class="diff-line-num new_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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<pre style="margin: 0;"> <span id="LC1529" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1463
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<td class="diff-line-num new_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="plaintext">Proper normalization is important as it ensures that other sources of</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1507" style="width: 35px; color: rgba(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="1574" style="width: 35px; color: rgba(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">@@ -1507,14 +1574,14 @@ briefly described below:</td>
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1507
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<td class="diff-line-num new_line" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1574
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="plaintext"> No normalization is performed.</span>
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<td class="diff-line-num old_line" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1508
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<td class="diff-line-num new_line" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1575
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<pre style="margin: 0;"> <span id="LC1575" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1509
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<td class="diff-line-num new_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1576
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<pre style="margin: 0;"> <span id="LC1576" class="line" lang="plaintext">Command-line</span>
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1510
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<td class="diff-line-num new_line old" data-linenumber="1577" style="width: 35px; color: rgba(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="LC1510" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1511" style="width: 35px; color: rgba(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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1577
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="plaintext"><span class="idiff left right">------------</span></span>
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1511
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1578
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<pre style="margin: 0;"> <span id="LC1578" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1512
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<td class="diff-line-num new_line" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1579
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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="plaintext">In addition to choosing normalization for various analyses in the GUI,</span>
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1513
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1580
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<pre style="margin: 0;"> <span id="LC1580" class="line" lang="plaintext">you can also call Transit to normalize wig files from the command-line,</span>
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1514
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<td class="diff-line-num new_line" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1581
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<pre style="margin: 0;"> <span id="LC1581" class="line" lang="plaintext">as shown in this example:</span>
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<td class="diff-line-num old_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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1582
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<pre style="margin: 0;"> <span id="LC1582" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1516
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<td class="diff-line-num new_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1583
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<pre style="margin: 0;"> <span id="LC1583" class="line" lang="plaintext">Example</span>
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<td class="diff-line-num old old_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1517
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<td class="diff-line-num new_line old" data-linenumber="1584" style="width: 35px; color: rgba(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="LC1517" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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1584
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<pre style="margin: 0;">+<span id="LC1584" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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1518
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1585
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<pre style="margin: 0;"> <span id="LC1585" class="line" lang="plaintext"></span>
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1519
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1586
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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="plaintext">::</span>
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1520
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1587
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<pre style="margin: 0;"> <span id="LC1587" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1539" style="width: 35px; color: rgba(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="1606" style="width: 35px; color: rgba(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">@@ -1539,7 +1606,7 @@ If the input file is a combined_wig file, indicate it with a '-c' flag.</td>
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1539
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1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="plaintext"></span>
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1540
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1607
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="plaintext">.. rst-class:: transit_clionly</span>
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1541
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<td class="diff-line-num new_line" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1608
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<pre style="margin: 0;"> <span id="LC1608" class="line" lang="plaintext">Pathway Enrichment Analysis</span>
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1542
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<td class="diff-line-num new_line old" data-linenumber="1609" style="width: 35px; color: rgba(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="LC1542" class="line" lang="plaintext"><span class="idiff left right">---------------------------</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="plaintext"><span class="idiff left right">===========================</span></span>
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1543
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1610
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<pre style="margin: 0;"> <span id="LC1610" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1544
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<td class="diff-line-num new_line" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1611
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="plaintext">Pathway Enrichment Analysis provides a method to</span>
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1545
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1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="plaintext">identify enrichment of functionally-related genes among those that are</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1548" style="width: 35px; color: rgba(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="1615" style="width: 35px; color: rgba(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">@@ -1548,10 +1615,10 @@ significantly more or less essential between two conditions).</td>
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1548
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="plaintext">The analysis is typically applied as post-processing step to the hits identified</span>
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<td class="diff-line-num old_line" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1549
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="plaintext">by a comparative analysis, such as *resampling*.</span>
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1550
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1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="plaintext">Several analytical method are provided:</span>
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1551
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<pre style="margin: 0;">-<span id="LC1551" class="line" lang="plaintext">Fisher's exact test (hypergeometric distribution), GSEA (Gene Set Enrichment Analysis)</span>
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1618
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<pre style="margin: 0;">+<span id="LC1618" class="line" lang="plaintext">Fisher's exact test (<span class="idiff left right">FET, </span>hypergeometric distribution), GSEA (Gene Set Enrichment Analysis)</span>
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1552
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1619
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="plaintext">by `Subramanian et al (2005) <https://www.ncbi.nlm.nih.gov/pubmed/16199517>`_,</span>
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1553
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1620
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<pre style="margin: 0;"> <span id="LC1620" class="line" lang="plaintext">and `Ontologizer <https://www.ncbi.nlm.nih.gov/pubmed/17848398>`_.</span>
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1554
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<pre style="margin: 0;">-<span id="LC1554" class="line" lang="plaintext">For <span class="idiff left right">the Fisher</span> exact test, </span>
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1621
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<pre style="margin: 0;">+<span id="LC1621" class="line" lang="plaintext">For <span class="idiff left right">Fisher's</span> exact test, </span>
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1555
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1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="plaintext">genes in the resampling output file with adjusted p-value < 0.05 are taken as hits,</span>
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<td class="diff-line-num old_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1556
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<td class="diff-line-num new_line" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1623
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<pre style="margin: 0;"> <span id="LC1623" class="line" lang="plaintext">and evaluated for overlap with functional categories of genes.</span>
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1557
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<td class="diff-line-num new_line" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1624
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<pre style="margin: 0;"> <span id="LC1624" class="line" lang="plaintext">The GSEA methods use the whole list of genes, ranked in order of statistical significance</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1578,17 +1645,17 @@ and is not available in the Transit GUI.</td>
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1645
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="plaintext"></span>
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1579
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1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="plaintext"></span>
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1580
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1647
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="plaintext">Usage</span>
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1581
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<pre style="margin: 0;">-<span id="LC1581" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~</span></span>
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1648
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<pre style="margin: 0;">+<span id="LC1648" class="line" lang="plaintext"><span class="idiff left right">-----</span></span>
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1582
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1649
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="plaintext"></span>
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1583
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1650
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="plaintext">::</span>
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1584
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1651
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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="plaintext"></span>
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1585
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<pre style="margin: 0;">-<span id="LC1585" class="line" lang="plaintext"> python3 src/transit.py pathway_enrichment <resampling_file> <associations> <pathways> <output_file> [-M <F<span class="idiff left right">ISHER</span>|GSEA|ONT>] [-PC <int>]</span>
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1652
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<pre style="margin: 0;">+<span id="LC1652" class="line" lang="plaintext"> python3 src/transit.py pathway_enrichment <resampling_file> <associations> <pathways> <output_file> [-M <F<span class="idiff left right">ET</span>|GSEA|ONT>] [-PC <int>]</span>
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1586
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1653
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<pre style="margin: 0;"> <span id="LC1653" class="line" lang="plaintext"></span>
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1587
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1654
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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="plaintext">|</span>
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1588
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1655
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<pre style="margin: 0;"> <span id="LC1655" class="line" lang="plaintext"></span>
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1589
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1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="plaintext"></span>
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1590
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1657
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<pre style="margin: 0;"> <span id="LC1657" class="line" lang="plaintext">Parameters</span>
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1591
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<pre style="margin: 0;">-<span id="LC1591" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~</span></span>
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1658
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="plaintext"><span class="idiff left right">----------</span></span>
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1592
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1659
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="plaintext">- **Resampling File**</span>
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1593
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="plaintext"> The resampling file is the one obtained after using the resampling method in Transit. (It is a tab separated file with 11 columns.) GSEA method makes usage of the last column (adjusted P-value)</span>
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1594
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="plaintext">- **Associations File**</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1689" style="width: 35px; color: rgba(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">@@ -1622,14 +1689,18 @@ Parameters</td>
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1622
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<pre style="margin: 0;"> <span id="LC1689" class="line" lang="plaintext"> ...</span>
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1690
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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="plaintext">- **-M**</span>
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1625
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<pre style="margin: 0;">-<span id="LC1625" class="line" lang="plaintext"> Methodology to be used. F<span class="idiff left right">ISHER</span> is used by default (even without specifying -M).</span>
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<pre style="margin: 0;">+<span id="LC1692" class="line" lang="plaintext"> Methodology to be used. F<span class="idiff left right">ET</span> is used by default (even without specifying -M).</span>
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1693
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<pre style="margin: 0;"> <span id="LC1693" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC1627" class="line" lang="plaintext"> **F<span class="idiff left right">ISHER</span>**</span>
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1694
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="plaintext"> **F<span class="idiff left right">ET</span>**</span>
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<pre style="margin: 0;"> <span id="LC1695" class="line" lang="plaintext"> This implements Fisher's Exact Test (hypergeometric distribution) to determine a p-value for each pathway, based on the proportion of pathway member observed in list of hits (conditionally essential gene by resampling, padj<0.05) compared to the background proportion in the overall genome, and p-values are adjusted post-hoc by the Benjamini-Hochberg procedure to limit the FDR to 5%. </span>
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1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="plaintext"></span>
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1630
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1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="plaintext"> In the output file, an "enrichment score" is reported, which is the ratio of the observed number of pathway members among the hits to the expected number. Pseudocounts of 2 are included in the calculation to reduce the bias toward small pathways with only a few genes; this can be adjusted with the -PC flag (below).</span>
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1698
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<pre style="margin: 0;"> <span id="LC1698" class="line" lang="plaintext"></span>
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1632
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<pre style="margin: 0;">-<span id="LC1632" class="line" lang="plaintext"> FISHER can be used with GO terms.</span>
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1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="plaintext"> FET can be used with GO terms.</span>
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1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="plaintext"></span>
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1701
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<pre style="margin: 0;">+<span id="LC1701" class="line" lang="plaintext"> Additional flags for FET:</span>
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1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="plaintext"> - **-PC <int>**: Pseudocounts used in calculating the enrichment score and p-value by hypergeometic distribution. Default: PC=2.</span>
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1704
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<pre style="margin: 0;"> <span id="LC1704" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1705" class="line" lang="plaintext"> **GSEA**</span>
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1635
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<pre style="margin: 0;"> <span id="LC1706" class="line" lang="plaintext"> Gene Set Enrichment Analysis. GSEA assess the significance of a pathway by looking at how the members fall in the ranking of all genes. The genes are first ranked by significance from resampling. Specifically, they are sorted by signed-log-p-value, SLPV=sign(LFC)*(log(pval)), which puts them in order so that the most significant genes with negative LFC are at the top, the most significant with positive LFC are at the bottom, and insignificant genes fall in the middle. Roughly, GSEA computes the mean rank of pathway members, and evaluates significance based on a simulated a null distribution. p-values are again adjusted at the end by BH.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1638,17 +1709,58 @@ Parameters</td>
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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1710" class="line" lang="plaintext"> GSEA can be used with GO terms.</span>
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<pre style="margin: 0;"> <span id="LC1711" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1712" class="line" lang="plaintext"> Additional flags for GSEA:</span>
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<pre style="margin: 0;">+<span id="LC1713" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="plaintext"> - **-ranking SLPV|LFC**: method used to rank all genes; SLPV is signed-log-p-value (default); LFC is log2-fold-change from resampling</span>
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="plaintext"> - **-p <float>**: exponent to use in calculating enrichment score; recommend trying '-p 0' (default) or '-p 1' (as used in Subramaniam et al, 2005)</span>
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1717
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<pre style="margin: 0;">+<span id="LC1717" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="plaintext"> - **-Nperm <int>**: number of permutations to simulate for null distribution to determine p-value (default=10000)</span>
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<pre style="margin: 0;">+<span id="LC1719" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1720" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1721" class="line" lang="plaintext"> **ONT**</span>
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<pre style="margin: 0;">-<span id="LC1642" class="line" lang="plaintext"> Ontologizer is a specialized method for GO terms that takes parent-child relationships into account among nodes in the GO hierarchy. This can enhance the specificity of pathways detected as significant. Hierarhical relationships among GO terms are encoded in an OBO file, which is included in the src/pytransit/data/ directory.</span>
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="plaintext"> Ontologizer is a specialized method for GO terms that takes parent-child relationships into account among nodes in the GO hierarchy. This can enhance the specificity of pathways detected as significant. <span class="idiff left right">(The problem is that there are many GO terms in the hierarchy covering similar or identical sets of genes, and often, if one node is significantly enriched, then several of its ancestors will be too, which obscures the results with redundant hits; Ontologizer reduces the significance of nodes if their probability distribution among hits can be explained by their parents.) </span>Hierarhical relationships among GO terms are encoded in an OBO file, which is included in the src/pytransit/data/ directory.</span>
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<pre style="margin: 0;"> <span id="LC1723" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1724" class="line" lang="plaintext"> `Grossmann S, Bauer S, Robinson PN, Vingron M. Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics. 2007 Nov 15;23(22):3024-31. <https://www.ncbi.nlm.nih.gov/pubmed/17848398>`_</span>
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<pre style="margin: 0;"> <span id="LC1725" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC1646" class="line" lang="plaintext">- **-PC**</span>
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<pre style="margin: 0;">-<span id="LC1647" class="line" lang="plaintext"> Pseudocounts used in calculating enrichment score in output file for FISHER. Default: PC=2.</span>
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1729" class="line" lang="plaintext">Auxilliary Pathway Files in Transit Data Directory</span>
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<pre style="margin: 0;">+<span id="LC1730" class="line" lang="plaintext">--------------------------------------------------</span>
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1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="plaintext">These files for pathway analysis are distributed in the Transit data directory </span>
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<pre style="margin: 0;">+<span id="LC1735" class="line" lang="plaintext">(e.g. transit/src/pytransit/data/).</span>
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<pre style="margin: 0;">+<span id="LC1736" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1737" class="line" lang="plaintext">+----------+---------+--------------------+--------------------------------------+--------------------------------+</span>
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<pre style="margin: 0;">+<span id="LC1738" class="line" lang="plaintext">| system | num cats| applicable methods | associations of genes with roles | pathway definitions/role names |</span>
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1739
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="plaintext">+==========+=========+====================+======================================+================================+</span>
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<pre style="margin: 0;">+<span id="LC1740" class="line" lang="plaintext">| COG | 20 | FET*, GSEA | H37Rv_COG_roles.dat | COG_roles.dat |</span>
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1741
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<pre style="margin: 0;">+<span id="LC1741" class="line" lang="plaintext">+----------+---------+--------------------+--------------------------------------+--------------------------------+</span>
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<pre style="margin: 0;">+<span id="LC1742" class="line" lang="plaintext">| Sanger | 153 | FET*, GSEA* | H37Rv_sanger_roles.dat | sanger_roles.dat |</span>
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1743
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="plaintext">+----------+---------+--------------------+--------------------------------------+--------------------------------+</span>
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="plaintext">| GO | 2545 | FET, GSEA | H37Rv_GO_terms.txt | GO_term_names.dat |</span>
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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="plaintext">+----------+---------+--------------------+--------------------------------------+--------------------------------+</span>
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="plaintext">| | | ONT* | GO_terms_for_each_Rv.obo-3-11-18.txt | gene_ontology.1_2.3-11-18.obo |</span>
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1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="plaintext">+----------+---------+--------------------+--------------------------------------+--------------------------------+</span>
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1748
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<pre style="margin: 0;">+<span id="LC1748" class="line" lang="plaintext"></span>
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1749
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="plaintext">asterisk means 'recommended' combination of method with system of functional categories</span>
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1750
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="plaintext"></span>
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1751
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<pre style="margin: 0;">+<span id="LC1751" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1752" class="line" lang="plaintext">Current Recommendations</span>
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1753
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="plaintext">-----------------------</span>
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1754
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1755" class="line" lang="plaintext">Here are the recommended combinations of pathway methods to use for different systems of functional categories:</span>
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1756
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<pre style="margin: 0;">+<span id="LC1756" class="line" lang="plaintext"></span>
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1757
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<pre style="margin: 0;">+<span id="LC1757" class="line" lang="plaintext"> * For COG, use '-M FET'</span>
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1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="plaintext"> * For Sanger roles, try both FET and GSEA</span>
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1759
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<pre style="margin: 0;">+<span id="LC1759" class="line" lang="plaintext"> * For GO terms, use 'M -ONT'</span>
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1648
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1760
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<pre style="margin: 0;"> <span id="LC1760" class="line" lang="plaintext"></span>
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1649
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1761
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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="plaintext"></span>
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1650
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<pre style="margin: 0;"> <span id="LC1762" class="line" lang="plaintext">Examples</span>
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<pre style="margin: 0;">-<span id="LC1651" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~</span></span>
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1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="plaintext"><span class="idiff left right">--------</span></span>
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1764
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<pre style="margin: 0;"> <span id="LC1764" class="line" lang="plaintext"></span>
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1765
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<pre style="margin: 0;"> <span id="LC1765" class="line" lang="plaintext">::</span>
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1766
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<pre style="margin: 0;"> <span id="LC1766" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1667,7 +1779,7 @@ Examples</td>
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<pre style="margin: 0;"> <span id="LC1779" class="line" lang="plaintext"> # Ontologizer is a specialized method for GO terms</span>
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="plaintext"> > transit pathway_enrichment resampling_glyc_chol.txt $DATA/H37Rv_GO_terms.txt $DATA/GO_term_names.dat pathways_Ontologizer.txt -M ONT</span>
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1669
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1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="plaintext"></span>
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1670
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<pre style="margin: 0;">-<span id="LC1670" class="line" lang="plaintext">The $DATA environment variable i<span class="idiff left right">s</span> these examples refers to the Transit data directory, e.g. src/pytransit/data/.</span>
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1782
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<pre style="margin: 0;">+<span id="LC1782" class="line" lang="plaintext">The $DATA environment variable i<span class="idiff left right">n</span> these examples refers to the Transit data directory, e.g. src/pytransit/data/.</span>
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1671
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<pre style="margin: 0;"> <span id="LC1783" class="line" lang="plaintext"></span>
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1672
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1784
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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="plaintext">.. rst-class:: transit_sectionend</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1679,7 +1791,7 @@ The $DATA environment variable is these examples refers to the Transit data dire</td>
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1792" class="line" lang="plaintext">.. rst-class:: transit_clionly</span>
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<pre style="margin: 0;"> <span id="LC1793" class="line" lang="plaintext">tnseq_stats</span>
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1682
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<pre style="margin: 0;">-<span id="LC1682" class="line" lang="plaintext"><span class="idiff left right">-----------</span></span>
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<pre style="margin: 0;">+<span id="LC1794" class="line" lang="plaintext"><span class="idiff left right">===========</span></span>
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<pre style="margin: 0;"> <span id="LC1795" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1796" class="line" lang="plaintext">You can generate the same table to statistics as on the Quality Control panel in the GUI</span>
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<pre style="margin: 0;"> <span id="LC1797" class="line" lang="plaintext">from the command-line using the 'tnseq_stats' command. Here is an example:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1710,7 +1822,7 @@ from the command-line using the 'tnseq_stats' command. Here is an example:</td>
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<pre style="margin: 0;"> <span id="LC1822" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1823" class="line" lang="plaintext">.. rst-class:: transit_clionly</span>
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1824
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<pre style="margin: 0;"> <span id="LC1824" class="line" lang="plaintext">corrplot</span>
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1713
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<td class="diff-line-num new_line old" data-linenumber="1825" style="width: 35px; color: rgba(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="LC1713" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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1825
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<pre style="margin: 0;">+<span id="LC1825" class="line" lang="plaintext"><span class="idiff left right">========</span></span>
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1714
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1826
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<pre style="margin: 0;"> <span id="LC1826" class="line" lang="plaintext"></span>
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1715
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<td class="diff-line-num new_line" data-linenumber="1827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1827
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<pre style="margin: 0;"> <span id="LC1827" class="line" lang="plaintext">A useful tool when evaluating the quality of a collection of TnSeq datasets is to make a </span>
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1716
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1828
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<pre style="margin: 0;"> <span id="LC1828" class="line" lang="plaintext">*correlation plot* of the mean insertion counts (averaged at the gene-level) among samples. </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1725" style="width: 35px; color: rgba(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="1837" style="width: 35px; color: rgba(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">@@ -1725,7 +1837,7 @@ and relies on the 'corrplot' R package.</td>
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1725
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1837
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<pre style="margin: 0;"> <span id="LC1837" class="line" lang="plaintext">See :ref:`Installation Instructions <install-zinb>`.</span>
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1726
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1838
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<pre style="margin: 0;"> <span id="LC1838" class="line" lang="plaintext"></span>
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1727
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<td class="diff-line-num new_line" data-linenumber="1839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1839
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<pre style="margin: 0;"> <span id="LC1839" class="line" lang="plaintext">Usage:</span>
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1728
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<pre style="margin: 0;">-<span id="LC1728" class="line" lang="plaintext"><span class="idiff left right">~~~~~~</span></span>
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1840
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<pre style="margin: 0;">+<span id="LC1840" class="line" lang="plaintext"><span class="idiff left right">------</span></span>
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1729
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1841
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<pre style="margin: 0;"> <span id="LC1841" class="line" lang="plaintext"></span>
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1730
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1842
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<pre style="margin: 0;"> <span id="LC1842" class="line" lang="plaintext">::</span>
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1731
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1843
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<pre style="margin: 0;"> <span id="LC1843" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1791" style="width: 35px; color: rgba(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="1903" style="width: 35px; color: rgba(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">@@ -1791,7 +1903,7 @@ to be installed on your system. See :ref:`Installation Instructions <install-zi</td>
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1791
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1903
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<pre style="margin: 0;"> <span id="LC1903" class="line" lang="plaintext"></span>
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1792
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1904
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<pre style="margin: 0;"> <span id="LC1904" class="line" lang="plaintext">.. rst-class:: transit_clionly</span>
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1793
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1905
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<pre style="margin: 0;"> <span id="LC1905" class="line" lang="plaintext">heatmap</span>
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1794
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<td class="diff-line-num new_line old" data-linenumber="1906" style="width: 35px; color: rgba(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="LC1794" class="line" lang="plaintext"><span class="idiff left right">-------</span></span>
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1906
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<pre style="margin: 0;">+<span id="LC1906" class="line" lang="plaintext"><span class="idiff left right">=======</span></span>
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1795
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1907
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<pre style="margin: 0;"> <span id="LC1907" class="line" lang="plaintext"></span>
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1796
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<td class="diff-line-num new_line" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1908
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<pre style="margin: 0;"> <span id="LC1908" class="line" lang="plaintext">The output of ANOVA or ZINB can be used to generate a heatmap that</span>
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1797
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<td class="diff-line-num new_line" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1909
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<pre style="margin: 0;"> <span id="LC1909" class="line" lang="plaintext">simultaneously clusters the significant genes and clusters the conditions,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1803" style="width: 35px; color: rgba(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="1915" style="width: 35px; color: rgba(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">@@ -1803,21 +1915,27 @@ and relies on the 'gplots' R package.</td>
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1803
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1915
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<pre style="margin: 0;"> <span id="LC1915" class="line" lang="plaintext">See :ref:`Installation Instructions <install-zinb>`.</span>
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1804
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1916
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<pre style="margin: 0;"> <span id="LC1916" class="line" lang="plaintext"></span>
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1805
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1917
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<pre style="margin: 0;"> <span id="LC1917" class="line" lang="plaintext">Usage:</span>
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1806
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<pre style="margin: 0;">-<span id="LC1806" class="line" lang="plaintext"><span class="idiff left right">~~~~~~</span></span>
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1918
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<pre style="margin: 0;">+<span id="LC1918" class="line" lang="plaintext"><span class="idiff left right">------</span></span>
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1807
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1919
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<pre style="margin: 0;"> <span id="LC1919" class="line" lang="plaintext"></span>
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1808
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1920
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<pre style="margin: 0;"> <span id="LC1920" class="line" lang="plaintext">::</span>
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1809
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1921
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<pre style="margin: 0;"> <span id="LC1921" class="line" lang="plaintext"></span>
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1810
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<pre style="margin: 0;">-<span id="LC1810" class="line" lang="plaintext"> python3 src/transit.py heatmap <span class="idiff left right">-anova|-zinb <anova_or_zinb_output> <heatmap.png></span></span>
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1922
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<pre style="margin: 0;">+<span id="LC1922" class="line" lang="plaintext"> python3 src/transit.py heatmap <span class="idiff left right"><anova_or_zinb_output> <heatmap.png> -anova|-zinb [-topk <int>] [-qval <float]</span></span>
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1811
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1923
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<pre style="margin: 0;"> <span id="LC1923" class="line" lang="plaintext"></span>
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1812
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<pre style="margin: 0;">-<span id="LC1812" class="line" lang="plaintext">Note that the <span class="idiff left right">*first* argument</span> is required to be either '-anova' or '-zinb', a flag to</span>
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1924
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<pre style="margin: 0;">+<span id="LC1924" class="line" lang="plaintext">Note that the <span class="idiff left right">first optional argument (flag)</span> is required to be either '-anova' or '-zinb', a flag to</span>
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1813
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1925
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<pre style="margin: 0;"> <span id="LC1925" class="line" lang="plaintext">indicate the type of file being provided as the second argument.</span>
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1814
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1926
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<pre style="margin: 0;"> <span id="LC1926" class="line" lang="plaintext"></span>
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1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="plaintext">By default, genes are selected for the heatmap based on qval<0.05.</span>
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1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="plaintext">However, the user may change the selection of genes through 2 flags:</span>
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1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="plaintext"></span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="plaintext"> * **-qval <float>**: change qval threshold for selecting genes (default=0.05)</span>
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1931
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<pre style="margin: 0;">+<span id="LC1931" class="line" lang="plaintext"> * **-topk <int>**: select top k genes ranked by significance (qval)</span>
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1932
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<pre style="margin: 0;">+<span id="LC1932" class="line" lang="plaintext"></span>
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1815
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="plaintext">Here is an example which generates the following image showing the similarities among</span>
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1816
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1934
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<pre style="margin: 0;"> <span id="LC1934" class="line" lang="plaintext">several different growth conditions:</span>
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1817
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1935
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<pre style="margin: 0;"> <span id="LC1935" class="line" lang="plaintext"></span>
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1818
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1936
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<pre style="margin: 0;"> <span id="LC1936" class="line" lang="plaintext">::</span>
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1819
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1937
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<pre style="margin: 0;"> <span id="LC1937" class="line" lang="plaintext"></span>
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1820
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<pre style="margin: 0;">-<span id="LC1820" class="line" lang="plaintext"> > python3 src/transit.py heatmap <span class="idiff left right">-anova anova_iron.txt heatmap_iron_anova.png</span></span>
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<pre style="margin: 0;">+<span id="LC1938" class="line" lang="plaintext"> > python3 src/transit.py heatmap <span class="idiff left right">anova_iron.txt heatmap_iron_anova.png -anova</span></span>
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1939
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<pre style="margin: 0;"> <span id="LC1939" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1940" class="line" lang="plaintext">.. image:: _images/iron_heatmap_anova_rotated.png</span>
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<pre style="margin: 0;"> <span id="LC1941" class="line" lang="plaintext"> :width: 1000</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1826,7 +1944,7 @@ several different growth conditions:</td>
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1944
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<pre style="margin: 0;"> <span id="LC1944" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1945" class="line" lang="plaintext">Importantly, the heatmap is based only on the subset of genes</span>
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1946
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<pre style="margin: 0;"> <span id="LC1946" class="line" lang="plaintext">identified as significantly varying (Padj < 0:05, typically only a few</span>
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<pre style="margin: 0;">-<span id="LC1829" class="line" lang="plaintext">hundred) in order to enhance the patterns, since otherwise they would</span>
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<pre style="margin: 0;">+<span id="LC1947" class="line" lang="plaintext">hundred<span class="idiff left right"> genes</span>) in order to enhance the patterns, since otherwise they would</span>
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1948
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<pre style="margin: 0;"> <span id="LC1948" class="line" lang="plaintext">be washed out by the rest of the genes in the genome, the majority of</span>
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<pre style="margin: 0;"> <span id="LC1949" class="line" lang="plaintext">which usually do not exhibit significant variation in counts.</span>
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1950
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<pre style="margin: 0;"> <span id="LC1950" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#1e85e527482a20741c2118e954cce9ba93cbe299"><strong>src/pytransit/export/mean_counts.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">@@ -61,6 +61,7 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC63" 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="LC64" class="line" lang="python"> <span class="n" style="color: #333;">combined_wig</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 class="n" style="color: #333;">ctrldata</span><span class="p">,</span></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;">annotation_path</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;">output_file</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(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">@@ -72,7 +73,7 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>
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73
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">SingleConditionMethod</span><span class="p">.</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;">description</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation_path</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">LOESS</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">LOESS</span><span class="p">,</span> <span class="n" style="color: #333;">NTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">CTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wxobj</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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 class="c1" style="color: #998; font-style: italic;"># boolean, interprete ctrldata as combined_wig file or comma-separated list of wig files?</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>
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<pre style="margin: 0;"> <span id="LC79" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,9 +111,10 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC111" 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;">output_path</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">output_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># could add a checkbox for combined_wig</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">combined_wig</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="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC115" 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;">ctrldata</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">(</span><span class="n" style="color: #333;">combined_wig</span><span class="p">,</span><span class="n" style="color: #333;">ctrldata</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;">annotationPath</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">normalization</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -124,8 +126,11 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC126" 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="LC127" 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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<pre style="margin: 0;"> <span id="LC128" 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="p">.</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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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ARGS="</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">args</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;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"KWARGS="</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">ctrldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC132" 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;">kwargs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"c"</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="LC133" class="line" lang="python"> <span class="n" style="color: #333;">ctrldata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">annotationPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">outpath</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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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outpath</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(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">@@ -136,7 +141,7 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">NTerminus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">CTerminus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC139" 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;">ctrldata</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC144" 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;">c<span class="idiff left">ombined_wig</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">c</span>trldata</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">annotationPath</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">normalization</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -152,9 +157,9 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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152
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> </span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Get orf data</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Getting Data"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fulldata</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tnseq_tools</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_data</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ctrldata</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fulldata</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">factors</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">norm_tools</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">normalize_data</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fulldata</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">normalization</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="idiff left right"> </span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">combined_wig</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fulldata</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">datasets</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tnseq_tools</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">read_combined_wig</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ctrldata</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fulldata</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tnseq_tools</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_data</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ctrldata</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fulldata</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">factors</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">norm_tools</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">normalize_data</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fulldata</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">normalization</span></span><span class="p"><span class="idiff right">,</span></span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">)</span></span>
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158
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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;">position</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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159
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"></span>
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160
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="nb" style="color: #0086b3;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transit_tools</span><span class="p">.</span><span class="n" style="color: #333;">get_pos_hash</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" style="width: 35px; color: rgba(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="176" style="width: 35px; color: rgba(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">@@ -171,16 +176,19 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"></span>
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172
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"></span>
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173
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Files:</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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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">:</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datasets</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">combined_wig</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span> </span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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175
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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="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</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="n" style="color: #333;">f</span><span class="p">)</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>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">K</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;">fulldata</span><span class="p">.</span><span class="n" style="color: #333;">shape</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get Gene objects</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">G</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="n" style="color: #333;">Genes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">,</span> <span class="n" style="color: #333;">norm</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">normalization</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">combined_wig</span><span class="p">:</span> <span class="n" style="color: #333;">G</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="n" style="color: #333;">Genes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">,</span> <span class="n" style="color: #333;">norm</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">normalization</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;">fulldata</span><span class="p">,</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">position</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">G</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="n" style="color: #333;">Genes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">,</span> <span class="n" style="color: #333;">norm</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">normalization</span><span class="p">)</span></span>
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181
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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;">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;">G</span><span class="p">)</span></span>
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182
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">progress_range</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">dataset_header</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="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">transit_tools</span><span class="p">.</span><span class="n" style="color: #333;">fetch_name</span><span class="p">(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">D</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">combined_wig</span><span class="p">:</span> <span class="n" style="color: #333;">dataset_header</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="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">datasets</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">dataset_header</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="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">transit_tools</span><span class="p">.</span><span class="n" style="color: #333;">fetch_name</span><span class="p">(</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">D</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">])</span></span>
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Orf</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Name</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Number of TA sites</span><span class="se" style="color: #d14;">\t</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="n" style="color: #333;">dataset_header</span><span class="p">)</span></span>
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185
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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;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">gene</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;">G</span><span class="p">):</span></span>
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186
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" style="width: 35px; color: rgba(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="212" style="width: 35px; color: rgba(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">@@ -204,7 +212,7 @@ class MeanCountsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC213" 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="LC214" 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="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""python %s export mean_counts <comma-separated .wig files><span class="idiff left right"> <annotation .prot_table> <output file></span>"""</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</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="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""python %s export mean_counts <comma-separated .wig files><span class="idiff left">|<combined_wig> <annotation .prot_table> <output file> [-c]</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff"> note: append -c if inputing a combined_wig file</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"""</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</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="LC216" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC218" 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="LC5" class="line" lang="plaintext"><TD><A HREF="H37Rv.fna">H37Rv.fna</A></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><TD><A HREF="H37Rv.prot_table">H37Rv.prot_table</A></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><TD>Stewart Cole's reference <I>M. tuberculosis</I> sequence (NC_000962.2)<TR></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><TD><A HREF="H37RvMA2.fna">H37RvMA2.fna</A></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><TD><A HREF="H37RvMA2.prot_table">H37RvMA2.prot_table</A></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><TD>Sequenced strain from the Sassetti lab, with</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> sequencing errors fixed (Ioerger et al. 2010;</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> http://www.ncbi.nlm.nih.gov/pubmed/20472797).<TR></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"><TD><A HREF="H37RvBD.fna">H37RvBD.fna</A></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"><TD><A HREF="H37RvBD.prot_table">H37RvBD.prot_table</A></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"><TD>Sequenced by the Broad Institute (NC_018143.2)<TR></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"><TD><A HREF="BCG.fna">BCG.fna</A></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"><TD><A HREF="BCG.prot_table">BCG.prot_table</A></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"><TD>Reference genome for <I>M. bovis</I> BCG (NC_008769.1)<TR></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"><TD><A HREF="mc2_155_tamu.fna">mc2_155_tamu.fna</A></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"><TD><A HREF="mc2_155_tamu.prot_table">mc2_155_tamu.prot_table</A></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"><TD><I>M. smegmattis</> mc2 155 sequenced at TAMU<TR></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"><A HREF="H37RvBD_mod3.prot_table">H37RvBD_mod3.prot_table</A></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"><TD>Annotation adjusted for an indel in the version of</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> the H37Rv Broad sequence used in the Sassetti lab (for</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> analyzing old datasets that have been previously processed</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> using this sequence).</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/5d32ed1fa55fe9aee4d1447851cbc57064cf6bdc...960097a9170f1d03b8b46705d8761b30742e1160#d0edb611a89a0dab9d0dc046d324f550b89d3d03"><strong>src/pytransit/transit_gui.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">@@ -382,10 +382,14 @@ class MainFrame ( wx.Frame ):</td>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">expLibSizer</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">expLibTip</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALIGN_CENTER_VERTICAL</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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383
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"></span>
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384
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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="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">nTermSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALIGN_CENTER_HORIZONTAL</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">cTermSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALIGN_CENTER_HORIZONTAL</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">ctrlLibSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALIGN_CENTER_HORIZONTAL</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">expLibSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALIGN_CENTER_HORIZONTAL</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#globalSizerVT.Add( nTermSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#globalSizerVT.Add( cTermSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#globalSizerVT.Add( ctrlLibSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )</span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#globalSizerVT.Add( expLibSizer, 1, wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 5 )</span></span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">nTermSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">cTermSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">ctrlLibSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">globalSizerVT</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span> <span class="n" style="color: #333;">expLibSizer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">../misc/test/tpp/H37Rv.fna</span></pre>
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