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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/tnseq-transit">Debian Med / tnseq-transit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f">bd6c5a95</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-12T16:15:41+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.2</pre>
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<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">
src/pytransit/__init__.py
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<li class="file-stats">
<a href="#ceace322bc3b80ee493350527cac7669ad632158">
src/pytransit/__main__.py
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<li class="file-stats">
<a href="#6063b8999118942a3c1455c39a0016742b0efe00">
src/pytransit/analysis/anova.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="#bc8898d1d2d3504ac8c72cd9edc38508899cca04">
src/pytransit/analysis/tn5gaps.py
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<li class="file-stats">
<a href="#07ca99dc668f43ea2451861342e18d287151cf0c">
src/pytransit/analysis/zinb.py
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<li class="file-stats">
<a href="#c77176f29141c0efdb023bb96c6e616ee90f9df8">
src/pytransit/convert/gff_to_prot_table.py
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<li class="file-stats">
<a href="#673b42bd3c9bfcd9bef1473ad7736494ed0ae4fe">
src/pytransit/doc/source/conf.py
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<li class="file-stats">
<a href="#66151ee5de4c4ddcc40088c69ef58e711fdb8af1">
src/pytransit/doc/source/index.rst
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<li class="file-stats">
<a href="#e4c47efb9db43431093096e67f5aab587b257ff4">
src/pytransit/doc/source/transit_methods.rst
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<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 +2,18 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">All notable changes to this project will be documented in this file.</span>
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<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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.2 2022-09-08</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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<td class="new_line diff-line-num new" 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> fixed bug in converting gff_to_prot_table</span>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p"> -</span> fixed bug in tn5gaps (fixes some false negative calls)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p"> -</span> fixed some bugs in pathway_enrichment (GSEA calculations)</span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> -</span> fixed links to Salmonella Tn5 data in docs</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p"> -</span> fixed problem with margins in heatmap.py that was causing R to fail </span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p"> -</span> added --ref to anova.py and zinb.py (for computing LFCs relative to designated reference condition)</span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p"> -</span> added --low_mean_filter for heatmap.py (for excluding genes with low counts, even if they are significant by ANOVA or ZINB)</span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> -</span> add dependency on pypubsub<4.0</span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"> </span>
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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(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="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.1 2020-12-22</span></span>
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(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="LC19" class="line" lang="markdown"><span class="p"> -</span> maintenance release</span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" style="width: 35px; color: rgba(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">@@ -148,7 +148,9 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># your project is installed. For an analysis of "install_requires" vs pip's</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># requirements files see:</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># https://packaging.python.org/en/latest/requirements.html</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'setuptools'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numpy~=1.16'</span><span class="p">,</span> <span class="s" style="color: #d14;">'scipy~=1.2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'matplotlib~=3.0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pillow~=6.0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'statsmodels~=0.9'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 'pypubsub<4.0' and 'wxPython' are needed for GUI only, but go ahead and install them</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the reason for restriction on pypubsub is that version>=4.0 does not work with python2 - I can probably get rid of this restriction, since everybody must be using python3 by now</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'setuptools'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numpy~=1.16'</span><span class="p">,</span> <span class="s" style="color: #d14;">'scipy~=1.2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'matplotlib~=3.0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pillow~=6.0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'statsmodels~=0.9'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pypubsub<4.0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wxPython'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#dependency_links = [</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "git+https://github.com/wxWidgets/wxPython.git#egg=wxPython"</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4"><strong>src/pytransit/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,6 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"transit_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tnseq_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"norm_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stat_tools"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.2.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.2.<span class="idiff left right">2</span>"</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[TRANSIT]"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#ceace322bc3b80ee493350527cac7669ad632158"><strong>src/pytransit/__main__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,11 +91,9 @@ def main(*args, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Tried GUI mode but has no wxPython</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">hasWx</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Please install wxPython to run in GUI Mode."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"To run in Console Mode please follow these instructions:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Please install wxPython to run in GUI Mode. (pip install wxPython)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: python %s <method>"</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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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"List of known methods:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"To run in Console Mode, try 'transit <method>' with one of the following methods:"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">methods</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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;"> - %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Running in Console mode</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#6063b8999118942a3c1455c39a0016742b0efe00"><strong>src/pytransit/analysis/anova.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">@@ -34,10 +34,11 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> anova</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="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;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">included_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">nterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</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;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" 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;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">included_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">nterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">cterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</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;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff right">[]</span>):</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">MultiConditionMethod</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="n" style="color: #333;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" 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;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">included_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">included_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">nterm</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nterm</span><span class="p">,</span> <span class="n" style="color: #333;">cterm</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cterm</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refs</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="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="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transit_error</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="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"error: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">msg</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># for some reason, transit_error() in base class or transit_tools doesn't work right; needs @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">@@ -58,18 +59,20 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC59" 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;">0.0</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">CTerminus</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;">"iC"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC61" 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="mi" style="color: #099;">5</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">refs</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;">"-ref"</span><span class="p">,[])</span> <span class="c1" style="color: #998; font-style: italic;"># list of condition names to use a reference for calculating LFCs</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">refs</span><span class="o" style="font-weight: 600;">!=</span><span class="p">[]:</span> <span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refs</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="LC64" class="line" lang="python"> <span class="n" style="color: #333;">ignored_conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="bp" style="color: #999;">None</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;">"-ignore-conditions"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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="LC65" class="line" lang="python"> <span class="n" style="color: #333;">included_conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="bp" style="color: #999;">None</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;">"-include-conditions"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check for unrecognized flags</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-n --ignore-conditions --include-conditions -iN -iC -PC"</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="LC68" class="line" lang="python"> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-n --ignore-conditions --include-conditions -iN -iC -PC<span class="idiff left right"> --ref</span>"</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="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rawargs</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arg</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;">and</span> <span class="n" style="color: #333;">arg</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;">flags</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_error</span><span class="p">(</span><span class="s" style="color: #d14;">"flag unrecognized: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">arg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">AnovaMethod</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="LC73" 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="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC72" 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;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">included_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">NTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">CTerminus</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="LC75" 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;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">included_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">NTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">CTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">PC</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">refs</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">wigs_to_conditions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">conditionsByFile</span><span class="p">,</span> <span class="n" style="color: #333;">filenamesInCombWig</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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="174" style="width: 35px; color: rgba(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">@@ -171,8 +174,9 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">rv</span><span class="p">],</span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">rv</span><span class="p">],</span><span class="n" style="color: #333;">statusMap</span><span class="p">[</span><span class="n" style="color: #333;">rv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pvals</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="n" style="color: #333;">qvals</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="n" style="color: #333;">status</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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;">statusMap</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>
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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;">calcLFCs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">means</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;">1</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;">grandmean</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;">means</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calcLFCs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">means</span><span class="p">,</span><span class="n" style="color: #333;">refs</span><span class="o" style="font-weight: 600;">=</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;">1</span><span class="p">):</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="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;">refs</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">means</span> <span class="c1" style="color: #998; font-style: italic;"># if ref condition(s) not explicitly defined, use mean of all</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;">grandmean</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;">refs</span><span class="p">)</span></span>
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176
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">lfcs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">((</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">grandmean</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">),</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">means</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lfcs</span></span>
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<pre style="margin: 0;"> <span id="LC182" 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">@@ -217,7 +221,8 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">Rv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"rv"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Rv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">MeansByRv</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">means</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">MeansByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">conditionsList</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">LFCs</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;">calcLFCs</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">,</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="LC224" class="line" lang="python"> <span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">MeansByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</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;">refs</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">LFCs</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;">calcLFCs</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">,</span><span class="n" style="color: #333;">refs</span><span class="p">,</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="LC226" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">([</span><span class="n" style="color: #333;">Rv</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">RvSiteindexesMap</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]))]</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"%0.2f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">means</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> </span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"%0.3f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">LFCs</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> </span>
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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">@@ -234,6 +239,7 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC239" 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="LC240" class="line" lang="python"><span class="s" style="color: #d14;"> --include-conditions <cond1,...> := Comma-separated list of conditions to use for analysis (Default: all)</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;"> --ignore-conditions <cond1,...> := Comma-separated list of conditions to ignore (Default: none)</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> --ref <cond> := which condition(s) to use as a reference for calculating LFCs (comma-separated if multiple conditions)</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;"> -iN <N> := Ignore TAs within given percentage (e.g. 5) of N terminus. Default: -iN 0</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"><span class="s" style="color: #d14;"> -iC <N> := Ignore TAs within given percentage (e.g. 5) of C terminus. Default: -iC 0</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"><span class="s" style="color: #d14;"> -PC <N> := pseudocounts to use for calculating LFC. Default: -PC 5"""</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">@@ -824,7 +824,7 @@ class GIMethod(base.QuadConditionMethod):</td>
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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 <span class="idiff left">M.A., Noueiry A., Sarkar D., Ahlquist P.</span> (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics, 5:155<span class="idiff right">–</span>176.</span></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 <span class="idiff left">et al</span> (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. <span class="idiff"> </span>Biostatistics, 5:155<span class="idiff right">-</span>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="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;">signif</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"BFDR"</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;">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;">sortedprobs</span><span class="p">)</span> </span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#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">@@ -112,6 +112,7 @@ class HeatmapMethod(base.SingleConditionMethod):</td>
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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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">low_mean_filter</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;">"low_mean_filter"</span><span class="p">,</span><span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># filter out genes with grandmean<5 by default</span></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="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="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC118" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,14 +137,18 @@ class HeatmapMethod(base.SingleConditionMethod):</td>
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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="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="LC138" 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="LC139" 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;">means</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="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="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="LC141" 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 LFCs</span></span>
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<pre style="margin: 0;"> <span id="LC142" 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="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="LC143" 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;"><span class="idiff left">means</span></span><span class="p"><span class="idiff right">,</span></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="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC145" 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="LC146" 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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<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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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,(</span><span class="n" style="color: #333;">w</span><span class="p">,</span><span class="n" style="color: #333;">means</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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<pre style="margin: 0;">+<span id="LC148" 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>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</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;">means</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="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mm</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;">low_mean_filter</span><span class="p">:</span> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"excluding %s/%s, mean(means)=%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="n" style="color: #333;">mm</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC153" 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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154
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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;">hits</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">@@ -168,8 +173,9 @@ H = 300+R*15</td>
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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="s" style="color: #d14;">png(outfilename,width=W,height=H)</span></span>
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170
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"><span class="s" style="color: #d14;">#defaults are lwid=lhei=c(1.5,4)</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;">heatmap.2(as.matrix(lfcs),col=colors,margin=c(12,12),lwid=c(2,6),lhei=c(0.1,2),trace="none",cexCol=1.4,cexRow=1.4,key=T) # make sure white=0</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;">heatmap.2(as.matrix(lfcs),col=colors,margin=c(12,12),lwid=c(2,6),lhei=c(0.1,2),trace="none",cexCol=1.4,cexRow=1.4,key=T) # make sure white=0</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"><span class="s" style="color: #d14;">#heatmap.2(as.matrix(lfcs),col=colors,margin=c(12,12),lwid=c(2,6),lhei=c(0.1,2),trace="none",cexCol=1.4,cexRow=1.4,key=T) # make sure white=0</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"><span class="s" style="color: #d14;">#heatmap.2(as.matrix(lfcs),col=colors,margin=c(12,12),trace="none",cexCol=1.2,cexRow=1.2,key=T) # make sure white=0 # setting margins was causing failures, so remove it 8/22/21</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"><span class="s" style="color: #d14;">heatmap.2(as.matrix(lfcs),col=colors,margin=c(12,12),trace="none",cexCol=1.2,cexRow=1.2,key=T) # actually, margins was OK, so the problem must have been with lhei and lwid</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"><span class="s" style="color: #d14;">dev.off()</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;">}</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"><span class="s" style="color: #d14;"> '''</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">@@ -177,7 +183,7 @@ dev.off()</td>
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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="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="LC185" 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="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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<pre style="margin: 0;">+<span id="LC186" 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 class="idiff left right"> [-low_mean_filter <int>]</span></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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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC189" 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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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#8e11d91610ba5cb2818cb8b617ccef1599a952fd"><strong>src/pytransit/analysis/pathway_enrichment.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,11 +160,14 @@ Optional parameters:</td>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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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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<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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<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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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># filter could be a subset of genes we want to focus on (throw out the rest)</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="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 class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC166" 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="LC167" 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="LC168" 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="LC169" 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="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">!=</span><span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</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="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">filter</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># skip genes in association file that are not relevant (i.e. not in resampling file)</span></span>
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<pre style="margin: 0;"> <span id="LC171" 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="LC172" 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="LC173" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -218,8 +221,11 @@ Optional parameters:</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">GSEA</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="LC223" 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="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 class="c1" style="color: #998; font-style: italic;"># hits are not used in GSEA()</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">orfs_in_resampling_file</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="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="LC225" 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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="LC222" 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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<pre style="margin: 0;">+<span id="LC226" 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 class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">orfs_in_resampling_file</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># bidirectional map; includes term->genelist and gene->termlist</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># filter: project associations (of orfs to pathways) onto only those orfs appearing in the resampling file</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">ontology</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_pathways</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pathwaysFile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">genenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC231" 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;">data</span><span class="p">:</span> <span class="n" style="color: #333;">genenames</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -235,14 +241,18 @@ Optional parameters:</td>
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<pre style="margin: 0;"> <span id="LC241" 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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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># note: genes with lowest p-val AND negative LFC have highest scores (like positive correlation)</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># there could be lots of ties with pval=0 or 1, but that's OK</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">LFC_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">"log2FC"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">Pval_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">"p-value"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC244" 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="c1" style="color: #998; font-style: italic;"># pair are: rv and score (SLPV)</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="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="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 class="n" style="color: #333;">orf</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>
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<pre style="margin: 0;">+<span id="LC247" 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>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">Pval_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">"p-value"</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;">Pval</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="n" style="color: #333;">Pval_col</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;">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="LC251" 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="LC252" 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>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">LFC_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">"log2FC"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">LFC</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="n" style="color: #333;">LFC_col</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;">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="LC256" 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;"># 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="LC258" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -260,23 +270,25 @@ Optional parameters:</td>
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<pre style="margin: 0;"> <span id="LC270" 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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271
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<pre style="margin: 0;"> <span id="LC271" 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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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">orfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">terms2orfs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">term</span><span class="p">,[])</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" 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;">orfs</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;">continue</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">num_genes_in_pathway</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;">orfs</span><span class="p">)</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num_genes_in_pathway</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># skip pathways with less than 2 genes</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">mr</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;">mean_rank</span><span class="p">(</span><span class="n" style="color: #333;">orfs</span><span class="p">,</span><span class="n" style="color: #333;">orfs2rank</span><span class="p">)</span></span>
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265
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">es</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;">enrichment_score</span><span class="p">(</span><span class="n" style="color: #333;">orfs</span><span class="p">,</span><span class="n" style="color: #333;">orfs2rank</span><span class="p">,</span><span class="n" style="color: #333;">orfs2score</span><span class="p">,</span><span class="n" style="color: #333;">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;">p</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># always positive, even if negative deviation, since I take abs</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">higher</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">Nperm</span><span class="p">):</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">perm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">allgenes</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">orfs</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># compare to ES for random sets of genes of same size</span></span>
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<pre style="margin: 0;">-<span id="LC269" 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;">enrichment_score</span><span class="p">(</span><span class="n" style="color: #333;">perm</span><span class="p">,</span><span class="n" style="color: #333;">orfs2rank</span><span class="p">,</span><span class="n" style="color: #333;">orfs2score</span><span class="p">,</span><span class="n" style="color: #333;">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;">p</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">es</span><span class="p">:</span> <span class="n" style="color: #333;">higher</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="LC270" 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;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">higher</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">10</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span> <span class="c1" style="color: #998; font-style: italic;"># adaptive</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">perm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">allgenes</span><span class="p">,</span><span class="n" style="color: #333;">num_genes_in_pathway</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># compare to enrichment score for random sets of genes of same size</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">e2</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;">enrichment_score</span><span class="p">(</span><span class="n" style="color: #333;">perm</span><span class="p">,</span><span class="n" style="color: #333;">orfs2rank</span><span class="p">,</span><span class="n" style="color: #333;">orfs2score</span><span class="p">,</span><span class="n" style="color: #333;">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;">p</span><span class="p">)</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e2</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">es</span><span class="p">:</span> <span class="n" style="color: #333;">higher</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">higher</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">10</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span> <span class="c1" style="color: #998; font-style: italic;"># adaptive: can stop after seeing 10 events (permutations with higher ES)</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">higher</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'#'</span><span class="p">,</span><span class="n" style="color: #333;">term</span><span class="p">,</span><span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">orfs</span></span><span class="p"><span class="idiff right">)</span>,</span><span class="n" style="color: #333;">mr</span><span class="p">,</span><span class="n" style="color: #333;">es</span><span class="p">,</span><span class="n" style="color: #333;">pval</span><span class="p">,</span><span class="n" style="color: #333;">ontology</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">term</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="LC284" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'#'</span><span class="p">,</span><span class="n" style="color: #333;">term</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">num_genes_in_pathway</span></span><span class="p">,</span><span class="n" style="color: #333;">mr</span><span class="p">,</span><span class="n" style="color: #333;">es</span><span class="p">,</span><span class="n" style="color: #333;">pval</span><span class="p">,</span><span class="n" style="color: #333;">ontology</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">term</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="LC285" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#sys.stderr.write(' '.join([str(x) for x in vals])+'\n')</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">pctg</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mf" style="color: #099;">100.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">Total</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Running Pathway Enrichment Method... %5.1f%%"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">pctg</span><span class="p">)</span></span>
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288
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<pre style="margin: 0;"> <span id="LC288" 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="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">term</span><span class="p">,</span><span class="n" style="color: #333;">mr</span><span class="p">,</span><span class="n" style="color: #333;">es</span><span class="p">,</span><span class="n" style="color: #333;">pval</span><span class="p">))</span></span>
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">results</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="LC291" class="line" lang="python"> <span class="n" style="color: #333;">results</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="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># sort on mean rank</span></span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">rej</span><span class="p">,</span><span class="n" style="color: #333;">qvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="p">[</span><span class="n" style="color: #333;">q</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">res</span><span class="p">,</span><span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span><span class="n" style="color: #333;">qvals</span><span class="p">)]</span></span>
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<li id="bc8898d1d2d3504ac8c72cd9edc38508899cca04">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#bc8898d1d2d3504ac8c72cd9edc38508899cca04"><strong>src/pytransit/analysis/tn5gaps.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="234" style="width: 35px; color: rgba(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="234" style="width: 35px; color: rgba(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">@@ -234,7 +234,7 @@ class Tn5GapsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC234" 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 Tn5 gaps method"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC235" 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="LC236" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC237" 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;">"<span class="idiff left right">Gett</span>ing data (May take a while)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC237" 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;">"<span class="idiff left right">Load</span>ing data (May take a while)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Combine all wigs</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span><span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transit_tools</span><span class="p">.</span><span class="n" style="color: #333;">get_validated_data</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="n" style="color: #333;">wxobj</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;">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">@@ -256,7 +256,7 @@ class Tn5GapsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">exp_cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exprunmax</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stddevrun</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get the runs</span></span>
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<pre style="margin: 0;">-<span id="LC259" 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;">"<span class="idiff left right">Gett</span>ing non-insertion runs in genome"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC259" 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;">"<span class="idiff left right">Identify</span>ing non-insertion runs in genome"</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;">run_arr</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;">runs_w_info</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="LC261" class="line" lang="python"> <span class="n" style="color: #333;">pos_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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<pre style="margin: 0;"> <span id="LC262" 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">@@ -275,13 +275,13 @@ class Tn5GapsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC275" 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="LC276" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="n" style="color: #333;">get_genes_in_range</span><span class="p">(</span><span class="n" style="color: #333;">pos_hash</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="p">[</span><span class="s" style="color: #d14;">'start'</span><span class="p">],</span> <span class="n" style="color: #333;">run</span><span class="p">[</span><span class="s" style="color: #d14;">'end'</span><span class="p">])</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="n" style="color: #333;">gene_orf</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="LC278" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes_obj</span><span class="p">[</span><span class="n" style="color: #333;">gene_orf</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># bug fix: moved this up</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">end</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">NTerminus</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">CTerminus</span></span>
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<pre style="margin: 0;"> <span id="LC281" 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;">strand</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;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">a</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</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;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">100.</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;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</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;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start</span><span class="p">)</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="mf" style="color: #099;">100.</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes_obj</span><span class="p">[</span><span class="n" style="color: #333;">gene_orf</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">inter_sz</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;">intersect_size</span><span class="p">([</span><span class="n" style="color: #333;">run</span><span class="p">[</span><span class="s" style="color: #d14;">'start'</span><span class="p">],</span> <span class="n" style="color: #333;">run</span><span class="p">[</span><span class="s" style="color: #d14;">'end'</span><span class="p">]],</span> <span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">])</span> <span class="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="LC286" class="line" lang="python"> <span class="n" style="color: #333;">percent_overlap</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;">calc_overlap</span><span class="p">([</span><span class="n" style="color: #333;">run</span><span class="p">[</span><span class="s" style="color: #d14;">'start'</span><span class="p">],</span> <span class="n" style="color: #333;">run</span><span class="p">[</span><span class="s" style="color: #d14;">'end'</span><span class="p">]],</span> <span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">run_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">[</span><span class="s" style="color: #d14;">'length'</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">@@ -296,9 +296,10 @@ class Tn5GapsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">results_per_gene</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="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">orf</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">inter_sz</span><span class="p">,</span> <span class="n" style="color: #333;">run_len</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="LC297" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Update Progress</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Running Tn5Gaps 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="n" style="color: #333;">N</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC300" 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="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">count</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="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">%</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Running Tn5Gaps 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="n" style="color: #333;">N</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC301" 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="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">results_per_gene</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">exp_run_len</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;">accum</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">N</span></span>
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<pre style="margin: 0;"> <span id="LC305" 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">@@ -331,9 +332,10 @@ class Tn5GapsMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC332" 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;">"#Essential gene count: %d</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;">sig_genes_count</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC333" 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;">"#Minimum reads: %d</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;">minread</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC334" 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;">"#Replicate combination method: %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;">replicates</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC335" 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;">"#Insertion density: %0.3f</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;">pins</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;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Mean run length: %0.1f</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;">exp_run_len</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;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Expected max run length: %0.1f</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;">exprunmax</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;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Minimum significant run length: %d</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;">min_sig_len</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC335" 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;">"#Expected run length: %1.5f</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;">exp_run_len</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;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Expected max run length: %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;">exprunmax</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC339" 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="LC340" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#self.output.write("#Orf\tName\tDesc\tk\tn\tr\tovr\tlenovr\tpval\tpadj\tcall\n")</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#07ca99dc668f43ea2451861342e18d287151cf0c"><strong>src/pytransit/analysis/zinb.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,7 +48,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> Zinb</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC51" 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;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">included_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">winz</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">nterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="n" style="color: #333;">cterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="n" style="color: #333;">condition</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Condition"</span><span class="p">,</span> <span class="n" style="color: #333;">covars</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</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;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC51" 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;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">included_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">winz</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">nterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="n" style="color: #333;">cterm</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="n" style="color: #333;">condition</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Condition"</span><span class="p">,</span> <span class="n" style="color: #333;">covars</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</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;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff right">[]</span>):</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">MultiConditionMethod</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="n" style="color: #333;">combined_wig</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC53" 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;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">included_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">included_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">nterm</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nterm</span><span class="p">,</span> <span class="n" style="color: #333;">cterm</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cterm</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">winz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">winz</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(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">@@ -56,6 +56,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interactions</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">condition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">condition</span></span>
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<pre style="margin: 0;"> <span id="LC58" 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>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refs</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC61" 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="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transit_error</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="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"error: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">msg</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># for some reason, transit_error() in base class or transit_tools doesn't work right; needs @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">@@ -92,19 +93,21 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">condition</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;">"-condition"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Condition"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">covars</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="bp" style="color: #999;">None</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;">"-covars"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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="LC95" class="line" lang="python"> <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="bp" style="color: #999;">None</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;">"-interactions"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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="LC96" class="line" lang="python"> <span class="n" style="color: #333;">refs</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;">"-ref"</span><span class="p">,[])</span> <span class="c1" style="color: #998; font-style: italic;"># list of condition names to use a reference for calculating LFCs</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">refs</span><span class="o" style="font-weight: 600;">!=</span><span class="p">[]:</span> <span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refs</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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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">winz</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"w"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">ignored_conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="bp" style="color: #999;">None</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;">"-ignore-conditions"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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="LC100" class="line" lang="python"> <span class="n" style="color: #333;">included_conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="bp" style="color: #999;">None</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;">"-include-conditions"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check for unrecognized flags</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-n --ignore-conditions --include-conditions -iN -iC -PC --condition --covars --interactions --gene"</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="LC103" class="line" lang="python"> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-n --ignore-conditions --include-conditions -iN -iC -PC --condition --covars --interactions --gene<span class="idiff left right"> --ref</span>"</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="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arg</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;">and</span> <span class="n" style="color: #333;">arg</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;">flags</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_error</span><span class="p">(</span><span class="s" style="color: #d14;">"flag unrecognized: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">arg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">ZinbMethod</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="LC108" 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="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC107" 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;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">included_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">winz</span><span class="p">,</span> <span class="n" style="color: #333;">NTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">CTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">condition</span><span class="p">,</span> <span class="n" style="color: #333;">covars</span><span class="p">,</span> <span class="n" style="color: #333;">interactions</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="LC110" 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;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">included_conditions</span><span class="p">,</span> <span class="n" style="color: #333;">winz</span><span class="p">,</span> <span class="n" style="color: #333;">NTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">CTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">condition</span><span class="p">,</span> <span class="n" style="color: #333;">covars</span><span class="p">,</span> <span class="n" style="color: #333;">interactions</span><span class="p">,</span> <span class="n" style="color: #333;">PC</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">refs</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">wigs_to_conditions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">conditionsByFile</span><span class="p">,</span> <span class="n" style="color: #333;">filenamesInCombWig</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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">@@ -615,9 +618,10 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"> <span class="n" style="color: #333;">Rv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"rv"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python"> <span class="n" style="color: #333;">means</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span></span>
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617
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> <span class="n" style="color: #333;">PC</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>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">LFCs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy</span><span class="p">.</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;">means</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">),</span><span class="mi" style="color: #099;">2</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">LFCs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy</span><span class="p">.</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;">means</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">),</span><span class="mi" style="color: #099;">2</span><span class="p">)]</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># still need to adapt this to use --ref if defined</span></span></span>
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<pre style="margin: 0;"> <span id="LC622" 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="LC620" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">means</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC623" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">refs</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">m</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;">means</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># grand mean across all conditions</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">([</span><span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">refs</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;">###TRI</span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">LFCs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">numpy</span><span class="p">.</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;">x</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">),</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">means</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">([</span><span class="n" style="color: #333;">Rv</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">RvSiteindexesMap</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">]))]</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"%0.1f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">statsByRv</span><span class="p">[</span><span class="n" style="color: #333;">Rv</span><span class="p">][</span><span class="s" style="color: #d14;">'mean'</span><span class="p">][</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">orderedStatGroupNames</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -638,6 +642,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC642" 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="LC643" class="line" lang="python"><span class="s" style="color: #d14;"> --ignore-conditions <cond1,cond2> := Comma separated list of conditions to ignore, for the analysis.</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"><span class="s" style="color: #d14;"> --include-conditions <cond1,cond2> := Comma separated list of conditions to include, for the analysis. Conditions not in this list, will be ignored.</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"><span class="s" style="color: #d14;"> --ref <cond> := which condition(s) to use as a reference for calculating LFCs (comma-separated if multiple conditions)</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"><span class="s" style="color: #d14;"> -iN <float> := Ignore TAs occuring within given percentage (as integer) of the N terminus. Default: -iN 5</span></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"><span class="s" style="color: #d14;"> -iC <float> := Ignore TAs occuring within given percentage (as integer) of the C terminus. Default: -iC 5</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python"><span class="s" style="color: #d14;"> -PC <N> := pseudocounts to use for calculating LFCs. Default: -PC 5</span></span>
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<li id="c77176f29141c0efdb023bb96c6e616ee90f9df8">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#c77176f29141c0efdb023bb96c6e616ee90f9df8"><strong>src/pytransit/convert/gff_to_prot_table.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">@@ -143,7 +143,7 @@ class GffProtMethod(base.ConvertMethod):</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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144
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<pre style="margin: 0;"> <span id="LC144" 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;">line</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;">lines</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;">line</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;">strip</span><span class="p">()</span></span>
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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="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</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="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</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">0</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</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="LC147" class="line" lang="python"> <span class="n" style="color: #333;">cols</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="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="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">9</span><span class="p">):</span> </span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">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;">"Ignoring invalid row with entries: {0}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cols</span><span class="p">)))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(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">@@ -160,6 +160,7 @@ class GffProtMethod(base.ConvertMethod):</td>
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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;">labels</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">Rv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">labels</span><span class="p">[</span><span class="s" style="color: #d14;">"locus_tag"</span><span class="p">].</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># error out if not found</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">labels</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'gene'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># or Name?</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene</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;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">labels</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'product'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span> </span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">desc</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">size</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="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">Rv</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="LC166" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writerow</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#673b42bd3c9bfcd9bef1473ad7736494ed0ae4fe"><strong>src/pytransit/doc/source/conf.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">@@ -34,7 +34,7 @@ extensions = [</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.todo'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.viewcode'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.napoleon'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.mathbase'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>'sphinx.ext.mathbase',</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.mathjax'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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">@@ -144,6 +144,15 @@ html_theme = 'sphinx_rtd_theme'</td>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># documentation.</span></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;">#html_theme_options = {}</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_theme_options = {</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'collapse_navigation': False,</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'sticky_navigation': True,</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'navigation_depth': 4,</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'includehidden': True,</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'titles_only': False</span></span>
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<pre style="margin: 0;">+<span id="LC153" 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="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain custom themes here, relative to this directory.</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_theme_path = []</span></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="384" style="width: 35px; color: rgba(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="393" style="width: 35px; color: rgba(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">@@ -384,5 +393,6 @@ epub_exclude_files = ['search.html']</td>
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384
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If false, no index is generated.</span></span>
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385
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#epub_use_index = True</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup</span><span class="p">(</span><span class="n" style="color: #333;">app</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;">app</span><span class="p">.</span><span class="n" style="color: #333;">add_stylesheet</span><span class="p">(</span><span class="s" style="color: #d14;">'css/default.css'</span><span class="p">)</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#app.add_stylesheet('css/default.css')</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">app</span><span class="p">.</span><span class="n" style="color: #333;">add_css_file</span><span class="p">(</span><span class="s" style="color: #d14;">'css/default.css'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"></span></pre>
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<li id="66151ee5de4c4ddcc40088c69ef58e711fdb8af1">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/bd6c5a95ac499539e7ccc1a567dd897a311cdf0f#66151ee5de4c4ddcc40088c69ef58e711fdb8af1"><strong>src/pytransit/doc/source/index.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,13 @@ Welcome to TRANSIT's documentation!</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> :target: https://github.com/mad-lab/transit</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> :alt: GitHub last tag</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">This page contains the documentation for TRANSIT. Below are a few quick links to some of the most important sections of the documentation, followed by a brief overview of TRANSIT's features.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Transit is python-based software for analyzing TnSeq data</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">(sequencing data from transposon mutant libraries)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">to determine essentiality of bacterial genes under different conditions.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">This page contains the documentation for TRANSIT. Below are a few</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">quick links to some of the most important sections of the</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">documentation, followed by a brief overview of TRANSIT's features.</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">Quick Links</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">~~~~~~~~~~~</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(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">@@ -20,7 +26,7 @@ Quick Links</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">* :ref:`tutorial-link`</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">* :ref:`tpp-link`</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">* :ref:`code-link`</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">* `PDF manual with overview of analysis methods in Transit <https://orca1.tamu.edu/essentiality/transit/transit-manual.pdf>`_</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">Features</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">@@ -57,8 +63,8 @@ TRANSIT offers a variety of features including:</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">.. _manual-link:</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">.. toctree::</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">2</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> :caption: TRANSIT M<span class="idiff left right">anual</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> :caption: TRANSIT M<span class="idiff left right">ANUAL</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> transit_overview</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> transit_install</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">@@ -70,7 +76,7 @@ TRANSIT offers a variety of features including:</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">.. _tutorial-link:</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">.. toctree::</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">2</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">3</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> :caption: TRANSIT Tutorials</span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> transit_essentiality_tutorial</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">@@ -83,7 +89,7 @@ TRANSIT offers a variety of features including:</td>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">.. _tpp-link:</span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">.. toctree::</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">2</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">3</span></span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> :caption: TPP Manual</span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> tpp.rst</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">@@ -91,7 +97,7 @@ TRANSIT offers a variety of features including:</td>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">.. _code-link:</span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">.. toctree::</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">2</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">3</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> :caption: Code Documentation</span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> transit</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">@@ -2,12 +2,16 @@</td>
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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="LC3" 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="LC5" class="line" lang="plaintext"> Analysis Methods<span class="idiff left right"> (Expand Me First!)</span></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="LC7" 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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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Below is a description of some of the methods.</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</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">**Tn5** datasets. Below is a description of some of the methods. </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">The analysis methods in Transit are also described in this `PDF manual</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><https://orca1.tamu.edu/essentiality/transit/transit-manual.pdf>`_ .</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></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">|</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">@@ -221,7 +225,7 @@ AK. (2009). `Simultaneous assay of every Salmonella Typhi gene using one million</td>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="plaintext">transposon mutants. <http://www.ncbi.nlm.nih.gov/pubmed/19826075>`_ *Genome Res.* , 19(12):2308-16.</span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext">This data was downloaded from SRA (located `here <http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000051>`_) , and used to make</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="plaintext">wig files (`base <http://orca1.tamu.edu/essentiality/transit/data/salmonella_base.wig>`_ and `bile <http://orca1.tamu.edu/essentiality/transit/data/salmonella_bile.wig>`_) and the following 4 baseline datasets</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">wig files (`base<span class="idiff left">line</span> <http://orca1.tamu.edu/essentiality/transit/data/salmonella_base<span class="idiff right">line</span>.wig>`_ and `bile <http://orca1.tamu.edu/essentiality/transit/data/salmonella_bile.wig>`_) and the following 4 baseline datasets</span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="plaintext">were merged to make a wig file: (IL2_2122_1,3,6,8). Our analysis</span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="plaintext">produced 415 genes with adjusted p-values less than 0.05, indicating</span>
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="plaintext">essentiality, and the analysis from the above paper produced 356</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">@@ -530,7 +534,7 @@ parameters are available for the method:</td>
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="plaintext"> calculated will have, at the expense of longer computation time. The</span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="plaintext"> resampling method runs on 10,000 samples by default.</span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="plaintext">- **Output Histograms:**<span class="idiff left right">\</span> Determines whether to output .png images of</span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext">- **Output Histograms:** Determines whether to output .png images of</span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="plaintext"> the histograms obtained from resampling the difference in</span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="plaintext"> read-counts.</span>
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<pre style="margin: 0;"> <span id="LC540" 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">@@ -552,7 +556,7 @@ parameters are available for the method:</td>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="plaintext"> as real differences. See the :ref:`Normalization <normalization>` section for a description</span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="plaintext"> of normalization method available in TRANSIT.</span>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="plaintext">- **<span class="idiff left">-</span>-ctrl_lib, <span class="idiff right">-</span>-exp_lib:** These are for doing resampling with datasets from multiple libraries, see below.</span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext">- **<span class="idiff left">\-\</span>-ctrl_lib, <span class="idiff right">\-\</span>-exp_lib:** These are for doing resampling with datasets from multiple libraries, see below.</span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="plaintext"></span>
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="plaintext">- **-iN, -iC:** Trimming of TA sites near N- and C-terminus.</span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="plaintext"> The default for trimming TA sites in the termini of ORFs is 0.</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">@@ -1051,6 +1055,7 @@ Example</td>
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="plaintext"> -n <string> := Normalization method. Default: -n TTR</span>
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="plaintext"> --ignore-conditions <cond1,...> := Comma separated list of conditions to ignore, for the analysis. Default: None</span>
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="plaintext"> --include-conditions <cond1,...> := Comma separated list of conditions to include, for the analysis. Default: All</span>
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="plaintext"> --ref <cond> := which condition(s) to use as a reference for calculating LFCs (comma-separated if multiple conditions)</span>
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="plaintext"> -iN <float> := Ignore TAs occurring within given percentage (as integer) of the N terminus. Default: -iN 0</span>
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="plaintext"> -iC <float> := Ignore TAs occurring within given percentage (as integer) of the C terminus. Default: -iC 0</span>
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="plaintext"> -PC := Pseudocounts to use in calculating LFCs. Default: -PC 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">@@ -1083,12 +1088,22 @@ The filenames should match what is shown in the header of the combined_wig (incl</td>
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="plaintext">Parameters</span>
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="plaintext">----------</span>
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1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="plaintext"></span>
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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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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="plaintext">The following parameters are available for the <span class="idiff left right">ANOVA </span>method:</span>
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1087
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="plaintext"></span>
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1088
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<pre style="margin: 0;">-<span id="LC1088" class="line" lang="plaintext">- **Ignore Conditions, Include Conditions:** Can use this to drop</span>
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1089
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<pre style="margin: 0;">-<span id="LC1089" class="line" lang="plaintext"> conditions not of interest or specify a particular subset of conditions to use for ANOVA analysis.</span>
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="plaintext">- **\-\-include-conditions:** Includes the given set of conditions from the ZINB test. Conditions not in this list are ignored. Note: this is useful for specifying the order in which the columns are listed in the output file.</span>
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1090
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1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="plaintext"></span>
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1091
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<pre style="margin: 0;">-<span id="LC1091" class="line" lang="plaintext">- **Normalization Method:** Determines which normalization method to</span>
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="plaintext">- **\-\-ignore-conditions:** Can use this to drop conditions not of interest.</span>
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="plaintext"></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="plaintext">- **\-\-ref:** Specify which condition to use as a reference for computing LFCs.</span>
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="plaintext"> By default, LFCs for each gene in each condition are calculated with respect</span>
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="plaintext"> to the *grand mean* count across all conditions (so conditions with higher counts will be balanced</span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="plaintext"> with conditions with lower counts). However, if there is a defined reference condition</span>
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="plaintext"> in the data, it may be specified using **\-\-ref** (in which case LFCs for that condition will</span>
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="plaintext"> be around 0, and will be positive or negative for the other conditions, depending on whether</span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="plaintext"> counts are higher or lower than the reference condintion. If there is more than one</span>
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="plaintext"> condition to use as reference (i.e. pooled), they may be given as a comma-separated list.</span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="plaintext"></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="plaintext">- **-n** Normalization Method. Determines which normalization method to</span>
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1092
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1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="plaintext"> use when comparing datasets. Proper normalization is important as it</span>
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1093
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="plaintext"> ensures that other sources of variability are not mistakenly treated</span>
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1094
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="plaintext"> as real differences. See the :ref:`Normalization <normalization>` section for a description</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1111" style="width: 35px; color: rgba(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">@@ -1096,6 +1111,8 @@ The following parameters are available for the method:</td>
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1096
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="plaintext"></span>
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1097
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="plaintext">- **-PC** Pseudocounts to use in calculating LFCs (see below). Default: -PC 5</span>
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1098
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="plaintext"></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="plaintext"></span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="plaintext"></span>
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1099
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="plaintext">Output and Diagnostics</span>
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1100
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="plaintext">----------------------</span>
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1101
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1118
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<pre style="margin: 0;"> <span id="LC1118" 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">@@ -1203,6 +1220,7 @@ Example</td>
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1203
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1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="plaintext"> -n <string> := Normalization method. Default: -n TTR</span>
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1204
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="plaintext"> --ignore-conditions <cond1,cond2> := Comma separated list of conditions to ignore, for the analysis. Default: None</span>
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1205
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="plaintext"> --include-conditions <cond1,cond2> := Comma separated list of conditions to include, for the analysis. Default: All</span>
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="plaintext"> --ref <cond> := which condition(s) to use as a reference for calculating LFCs (comma-separated if more than one)</span>
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1206
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1224
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<pre style="margin: 0;"> <span id="LC1224" class="line" lang="plaintext"> -iN <float> := Ignore TAs occuring within given percentage of the N terminus. Default: -iN 5</span>
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1207
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1225
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<pre style="margin: 0;"> <span id="LC1225" class="line" lang="plaintext"> -iC <float> := Ignore TAs occuring within given percentage of the C terminus. Default: -iC 5</span>
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1208
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1226
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="plaintext"> -PC <N> := Pseudocounts used in calculating LFCs in output file. Default: -PC 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">@@ -1265,8 +1283,9 @@ Parameters</td>
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1265
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1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="plaintext">The following parameters are available for the method:</span>
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1267
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="plaintext"></span>
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1268
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<pre style="margin: 0;">-<span id="LC1268" class="line" lang="plaintext">- **Ignore Conditions:** Ignores the given set of conditions from the ZINB test.</span>
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1269
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<pre style="margin: 0;">-<span id="LC1269" class="line" lang="plaintext">- **Include Conditions:** Includes the given set of conditions from the ZINB test. Conditions not in this list are ignored.</span>
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="plaintext">- **\-\-include-conditions:** Includes the given set of conditions from the ZINB test. Conditions not in this list are ignored. Note: this is useful for specifying the order in which the columns are listed in the output file.</span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="plaintext">- **\-\-ignore-conditions:** Ignores the given set of conditions from the ZINB test.</span>
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="plaintext">- **\-\-ref:** which condition to use as a reference when computing LFCs in the output file</span>
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="plaintext">- **Normalization Method:** Determines which normalization method to</span>
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="plaintext"> use when comparing datasets. Proper normalization is important as it</span>
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1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="plaintext"> ensures that other sources of variability are not mistakenly treated</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">@@ -1296,7 +1315,7 @@ strains (think: different 'slopes'). In such a case, we would say strain and tim</td>
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1296
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1315
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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="plaintext">If covariates distinguishing the samples are available,</span>
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="plaintext">such as batch or library, they may be</span>
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<pre style="margin: 0;">-<span id="LC1299" class="line" lang="plaintext">incorporated in the ZINB model by using the **\<span class="idiff left right">\-\</span>\-covars** flag and samples</span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="plaintext">incorporated in the ZINB model by using the **\<span class="idiff left right">-</span>\-covars** flag and samples</span>
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1300
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1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="plaintext">metadata file. For example, consider the following samples metadata</span>
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="plaintext">file, with a column describing the batch information of each</span>
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1302
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="plaintext">replicate.</span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1311,7 +1330,7 @@ replicate.</td>
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1311
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="plaintext"> chol2 cholesterol /Users/example_data/cholesterol_rep3.wig B2</span>
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1331
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="plaintext">This information can be included to eliminate variability due to batch by using</span>
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<pre style="margin: 0;">-<span id="LC1314" class="line" lang="plaintext">the **\<span class="idiff left right">\-\</span>\-covars** flag.</span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="plaintext">the **\<span class="idiff left right">-</span>\-covars** flag.</span>
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1315
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="plaintext"></span>
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1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="plaintext">::</span>
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1317
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<pre style="margin: 0;"> <span id="LC1336" 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">@@ -1319,7 +1338,7 @@ the **\\-\\-covars** flag.</td>
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1319
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1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="plaintext"></span>
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1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="plaintext"></span>
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1321
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="plaintext">Similarly, an interaction variable may be included in the model.</span>
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1322
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<pre style="margin: 0;">-<span id="LC1322" class="line" lang="plaintext">This is specified by the user with the **\<span class="idiff left right">\-\</span>\-interactions** flag,</span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="plaintext">This is specified by the user with the **\<span class="idiff left right">-</span>\-interactions** flag,</span>
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1323
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="plaintext">followed by the name of a column in the samples metadata to test as the interaction</span>
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="plaintext">with the condition. If there are multiple interactions, they may be given as a comma-separated list.</span>
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1336,7 +1355,7 @@ differs depending on the strain, we could do this:</td>
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1336
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1355
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="plaintext"> </span>
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1337
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="plaintext">In this case, the condition is implicitly assumed to be the column in the samples metadata file</span>
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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="plaintext">labeled 'Condition'. If you want to specify a different column to use as the primary condition to </span>
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<pre style="margin: 0;">-<span id="LC1339" class="line" lang="plaintext">test (for example, if Treatment were a distinct column), you can use the **\<span class="idiff left right">\-\</span>\-condition** flag:</span>
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="plaintext">test (for example, if Treatment were a distinct column), you can use the **\<span class="idiff left right">-</span>\-condition** flag:</span>
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1340
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1359
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="plaintext"></span>
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1341
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1360
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="plaintext">::</span>
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1342
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1361
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<pre style="margin: 0;"> <span id="LC1361" 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">@@ -1495,7 +1514,10 @@ typical threshold for conditional essentiality on is q-value < 0.05.</td>
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1495
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1514
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="plaintext">**LFCs** (log-fold-changes):</span>
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1496
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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="plaintext">For each condition, the LFC is calculated as the log-base-2 of the</span>
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1497
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="plaintext">ratio of mean insertion count in that condition **relative to the </span>
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1498
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<pre style="margin: 0;">-<span id="LC1498" class="line" lang="plaintext">mean of means across all the conditions**.</span>
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1517
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="plaintext">mean of means across all the conditions** (by default).</span>
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="plaintext">However, you can change this by desginating a specific reference condition using the flag **\-\-ref**.</span>
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="plaintext">(If there are multiple reference conditions, they may be given as a comma separated list.)</span>
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="plaintext">(If you are using interactions, it is more complicated to specify a reference condition by name because they have to include the interactions, e.g. as shown in the column headers in the output file.)</span>
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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="plaintext">Pseudocount are incorporated to reduce the impact of noise on LFCs, based on the formula below.</span>
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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="plaintext">The pseudocounts can be adjusted using the -PC flag.</span>
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="plaintext">Changing the pseudocounts (via -PC) can reduce the artifactual appearance of genes with</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">@@ -1723,7 +1745,26 @@ Parameters</td>
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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"> `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="LC1747" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1748" class="line" lang="plaintext"> For the ONT method in pathway_enrichment, the enrichment for a given</span>
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="plaintext"> GO term can be expressed (in a simplified way, leaving out the</span>
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="plaintext"> pseudocounts) as:</span>
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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">::</span>
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="plaintext"> enrichment = log ( (b/q) / (m/p) )</span>
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<pre style="margin: 0;">+<span id="LC1755" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;">+<span id="LC1756" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1757" class="line" lang="plaintext"> where:</span>
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1759" class="line" lang="plaintext">* b is the number of genes with this GO term in the subset of hits (e.g. conditional essentials from resampling, with qval<0.05)</span>
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="plaintext">* q is the number of genes in the subset of hits with a parent of this GO term</span>
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<pre style="margin: 0;">+<span id="LC1761" class="line" lang="plaintext">* m is the total number of genes with this GO term in the genome</span>
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="plaintext">* p is the number of genes in the genome with a parent of this GO term </span>
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="plaintext"> So enrichment is the log of the ratio of 2 ratios:</span>
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1726
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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"> 1. the relative abundance of genes with this GO term compared to those with a parent GO term among the hits</span>
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1767
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<pre style="margin: 0;">+<span id="LC1767" class="line" lang="plaintext"> 2. the relative abundance of genes with this GO term compared to those with a parent GO term in the whole genome</span>
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1768
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<pre style="margin: 0;"> <span id="LC1768" class="line" lang="plaintext"></span>
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1728
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1769
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<pre style="margin: 0;"> <span id="LC1769" class="line" lang="plaintext"></span>
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1729
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1770
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<pre style="margin: 0;"> <span id="LC1770" class="line" lang="plaintext">Auxilliary Pathway Files in Transit Data Directory</span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -1919,7 +1960,7 @@ Usage:</td>
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1919
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1960
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<pre style="margin: 0;"> <span id="LC1960" class="line" lang="plaintext"></span>
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1920
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1961
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<pre style="margin: 0;"> <span id="LC1961" class="line" lang="plaintext">::</span>
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1921
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1962
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<pre style="margin: 0;"> <span id="LC1962" class="line" lang="plaintext"></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 <anova_or_zinb_output> <heatmap.png> -anova|-zinb [-topk <int>] [-qval <float]</span>
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1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="plaintext"> python3 src/transit.py heatmap <anova_or_zinb_output> <heatmap.png> -anova|-zinb [-topk <int>] [-qval <float]<span class="idiff left right"> [-low_mean_filter <int>]</span></span>
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1923
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1964
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<pre style="margin: 0;"> <span id="LC1964" class="line" lang="plaintext"></span>
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1924
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1965
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<pre style="margin: 0;"> <span id="LC1965" class="line" lang="plaintext">Note that the first optional argument (flag) is required to be either '-anova' or '-zinb', a flag to</span>
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1925
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1966
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<pre style="margin: 0;"> <span id="LC1966" class="line" lang="plaintext">indicate the type of file being provided as the second argument.</span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1929,6 +1970,7 @@ However, the user may change the selection of genes through 2 flags:</td>
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1929
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1970
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<pre style="margin: 0;"> <span id="LC1970" class="line" lang="plaintext"></span>
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1930
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1971
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<pre style="margin: 0;"> <span id="LC1971" 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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1972
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<pre style="margin: 0;"> <span id="LC1972" class="line" lang="plaintext"> * **-topk <int>**: select top k genes ranked by significance (qval)</span>
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1973
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<pre style="margin: 0;">+<span id="LC1973" class="line" lang="plaintext"> * **-low_mean_filter <int>**: filter out genes with grand mean count (across all conditions) below this threshold (even if qval<0.05); default is to exclude genes with mean count<5</span>
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1932
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1974
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<pre style="margin: 0;"> <span id="LC1974" class="line" lang="plaintext"></span>
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1933
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1975
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<pre style="margin: 0;"> <span id="LC1975" class="line" lang="plaintext">Here is an example which generates the following image showing the similarities among</span>
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1934
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1976
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<pre style="margin: 0;"> <span id="LC1976" class="line" lang="plaintext">several different growth conditions:</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1985" style="width: 35px; color: rgba(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">@@ -1943,7 +1985,7 @@ several different growth conditions:</td>
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1943
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1985
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<pre style="margin: 0;"> <span id="LC1985" class="line" lang="plaintext"></span>
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1944
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1986
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<pre style="margin: 0;"> <span id="LC1986" class="line" lang="plaintext"></span>
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1945
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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC1987" class="line" lang="plaintext">Importantly, the heatmap is based only on the subset of genes</span>
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<td class="old_line diff-line-num old" data-linenumber="1946" 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">
1946
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<td class="new_line diff-line-num old" data-linenumber="1988" 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="LC1946" class="line" lang="plaintext">identified as significantly varying (Padj < 0:05, typically only a few</span>
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<td class="old_line diff-line-num new" data-linenumber="1947" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1988
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<pre style="margin: 0;">+<span id="LC1988" class="line" lang="plaintext">identified as <span class="idiff left">*</span>significantly varying<span class="idiff right">*</span> (Padj < 0:05, typically only a few</span>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC1989" class="line" lang="plaintext">hundred genes) in order to enhance the patterns, since otherwise they would</span>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1990
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<pre style="margin: 0;"> <span id="LC1990" class="line" lang="plaintext">be washed out by the rest of the genes in the genome, the majority of</span>
</pre>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC1991" class="line" lang="plaintext">which usually do not exhibit significant variation in counts.</span>
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