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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/tnseq-transit">Debian Med / tnseq-transit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295">fac26506</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-21T01:42:57+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.3</pre>
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<h4>13 changed files:</h4>
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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−
.travis.yml
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<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#88e0c8b85bd56c1ffb341f3c428ad72e4c8fc7c7">
src/pytpp/tpp_tools.py
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<li class="file-stats">
<a href="#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4">
src/pytransit/__init__.py
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<li class="file-stats">
<a href="#6063b8999118942a3c1455c39a0016742b0efe00">
src/pytransit/analysis/anova.py
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<li class="file-stats">
<a href="#a067391127fae50dcf63c3968bd732956357ed52">
src/pytransit/analysis/base.py
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<li class="file-stats">
<a href="#a522d0d990a6ccfbb24eba81a727b32c79e5f81a">
src/pytransit/analysis/gumbel.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="#a34f0a90fb53810325ed1916b277f5e963b763fb">
src/pytransit/data/samples_metadata_cg_covar.txt
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<li class="file-stats">
<a href="#e4c47efb9db43431093096e67f5aab587b257ff4">
src/pytransit/doc/source/transit_methods.rst
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<li class="file-stats">
<a href="#2db304110a376933b3ccb003bd122d724bfb8159">
src/pytransit/stat_tools.py
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<li class="file-stats">
<a href="#d89b43ded7022712aee60a6466cbc62fe14a73a3">
src/pytransit/tnseq_tools.py
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<li class="file-stats">
<a href="#8932e01e75ea1b89ecb1e441751d55c66ddb844e">
tests/test_tpp.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">services</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="6" 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="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker build -t transit .</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"></span>
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<td class="old_line diff-line-num old" data-linenumber="9" 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="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">DISPLAY</span><span class="pi">:</span> <span class="m" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_success</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span> <span class="c1" style="color: #998; font-style: italic;"># default: change</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span> <span class="c1" style="color: #998; font-style: italic;"># default: always</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">travis_wait 20 docker run -t transit</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"></span></pre>
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<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</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">@@ -2,8 +2,15 @@</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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.2 2022-09-08</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.3 2021-10-16</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p"> -</span> added Binomial essentials (EB) to Gumbel analysis (supplementing genes categorized as E), to help with low-saturation datasets</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p"> -</span> modified ANOVA and ZINB so that --include-conditions and --exclude-conditions refer to original Conditions column in samples metadata file (instead of whatever is specified by --conditions) </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"> </span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TPP:</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> -</span> improved metrics reported in <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>.tn_stats by TPP, to help diagnose why reads don't map</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"> </span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.2 2021-09-08</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p"> -</span> fixed bug in converting gff_to_prot_table</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p"> -</span> fixed bug in tn5gaps (fixes some false negative calls)</span>
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<li id="88e0c8b85bd56c1ffb341f3c428ad72e4c8fc7c7">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#88e0c8b85bd56c1ffb341f3c428ad72e4c8fc7c7"><strong>src/pytpp/tpp_tools.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="310" style="width: 35px; color: rgba(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="310" style="width: 35px; color: rgba(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">@@ -310,7 +310,7 @@ def extract_staggered(infile,outfile,vars):</td>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">output_failed</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># [WM] [add]</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">tot_tgtta</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="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Input files did not contain any reads matching prefix sequence with %d mismatches"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">mm1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">tot_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tot</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("[tn_preprocess]",s)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="511" style="width: 35px; color: rgba(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="511" style="width: 35px; color: rgba(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">@@ -511,7 +511,7 @@ def template_counts(ref,sam,bcfile,vars):</td>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">genome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_genome</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">replicon_index</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">genome</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="LC513" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if genome[i:i+2].upper()=="TA":</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">transposon</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Himar1"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">genome</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">"TA"</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="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">transposon</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Himar1"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">genome</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">"TA"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC515" 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="LC516" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hits</span><span class="p">[</span><span class="n" style="color: #333;">replicon_names</span><span class="p">[</span><span class="n" style="color: #333;">replicon_index</span><span class="p">]].</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">pos</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">@@ -1100,20 +1100,7 @@ def generate_output(vars):</td>
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="python"> <span class="n" style="color: #333;">FR_corr</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">cur_FR_corr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="python"> <span class="n" style="color: #333;">BC_corr</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">cur_BC_corr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="python"> <span class="n" style="color: #333;">primer</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTAGAGGGCCCAATTCGCCCTATAGTGAGT"</span></span>
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<pre style="margin: 0;">-<span id="LC1104" class="line" lang="python"> <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTAGACCGTCCAGTCTGGCAGGCCGGAAAC"</span></span>
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<pre style="margin: 0;">-<span id="LC1105" class="line" lang="python"> <span class="n" style="color: #333;">adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GATCGGAAGAGCACACGTCTGAACTCCAGTCAC"</span></span>
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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="python"> <span class="n" style="color: #333;">Himar1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACTTATCAGCCAACCTGTTA"</span></span>
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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="python"> <span class="n" style="color: #333;">tot_reads</span><span class="p">,</span><span class="n" style="color: #333;">nprimer</span><span class="p">,</span><span class="n" style="color: #333;">nvector</span><span class="p">,</span><span class="n" style="color: #333;">nadapter</span><span class="p">,</span><span class="n" style="color: #333;">misprimed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC1108" 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="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">reads1</span><span class="p">):</span></span>
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1109
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<pre style="margin: 0;">-<span id="LC1109" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'>'</span><span class="p">:</span> <span class="n" style="color: #333;">tot_reads</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC1110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">primer</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">nprimer</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1111
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<pre style="margin: 0;">-<span id="LC1111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vector</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">nvector</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1112
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<pre style="margin: 0;">-<span id="LC1112" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">nadapter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1113
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<pre style="margin: 0;">-<span id="LC1113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if "TGTTA" in line and Himar1 not in line: misprimed += 1</span></span>
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1114
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<td class="new_line diff-line-num old" data-linenumber="1103" 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="LC1114" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># basically, these should correspond to insertions at non-TA sites (so the terminal TA of ...TGTTA will be different)</span></span>
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1115
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<pre style="margin: 0;">-<span id="LC1115" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Himar1</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Himar1</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;">line</span><span class="p">:</span> <span class="n" style="color: #333;">misprimed</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span> </span>
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1116
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<td class="new_line diff-line-num old" data-linenumber="1103" 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="LC1116" class="line" lang="python"></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="python"> <span class="n" style="color: #333;">tot_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">tot_reads</span></span>
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1117
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="python"> <span class="n" style="color: #333;">read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_read_length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".reads1"</span><span class="p">)</span></span>
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1118
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1105
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="python"> <span class="n" style="color: #333;">mean_r1_genomic</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_genomic_portion</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".trimmed1"</span><span class="p">)</span></span>
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1119
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1106
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">single_end</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;">mean_r2_genomic</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_genomic_portion</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".genomic2"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1133,7 +1120,7 @@ def generate_output(vars):</td>
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1133
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="python"> <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;">'# ref_genome: %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="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">ref</span><span class="p">)</span></span>
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1134
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="python"> <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;">'# replicon_ids: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">replicon_ids</span><span class="p">))</span></span>
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1135
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1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="python"> <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;">"# total_reads (or read pairs): %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tot_reads</span><span class="p">)</span></span>
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1136
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<pre style="margin: 0;">-<span id="LC1136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">#</span>output.write("# truncated_reads %s (<span class="idiff right">fragmen</span>ts shorter than the read length; ADAP2 appears in read1)\n" % vars.truncated_reads)</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="python"> <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;">"# truncated_reads %s (<span class="idiff left right">genomic inser</span>ts shorter than the read length; ADAP2 appears in read1)</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="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">truncated_reads</span><span class="p">)</span></span>
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1137
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<td class="new_line diff-line-num" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="python"> <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;">"# trimmed_reads (reads with valid Tn prefix, and insert size>20bp): %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="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">tot_tgtta</span><span class="p">)</span></span>
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1138
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1125
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="python"> <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;">"# reads1_mapped: %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="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">r1</span><span class="p">)</span></span>
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1139
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1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="python"> <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;">"# reads2_mapped: %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="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">r2</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -1187,10 +1174,30 @@ def generate_output(vars):</td>
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1187
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1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="python"> <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;">"# FR_corr (Fwd templates vs. Rev templates): %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="n" style="color: #333;">FR_corr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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1188
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1175
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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="python"> <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;">"# BC_corr (reads vs. templates, summed over both strands): %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="n" style="color: #333;">BC_corr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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1189
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1176
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<pre style="margin: 0;"> <span id="LC1176" class="line" lang="python"></span>
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1190
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<td class="new_line diff-line-num old" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1190" class="line" lang="python"> <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;">"# primer_matches: %s reads (%0.1f%%) contain %s (Himar1)</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;">nprimer</span><span class="p">,</span><span class="n" style="color: #333;">nprimer</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">tot_reads</span><span class="p">),</span><span class="n" style="color: #333;">primer</span><span class="p">))</span></span>
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1191
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<td class="new_line diff-line-num old" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1191" class="line" lang="python"> <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;">"# vector_matches: %s reads (%0.1f%%) contain %s (phiMycoMarT7)</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;">nvector</span><span class="p">,</span><span class="n" style="color: #333;">nvector</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">tot_reads</span><span class="p">),</span><span class="n" style="color: #333;">vector</span><span class="p">))</span></span>
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1192
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<td class="new_line diff-line-num old" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1192" class="line" lang="python"> <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;">"# adapter_matches: %s reads (%0.1f%%) contain %s (Illumina/TruSeq index)</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;">nadapter</span><span class="p">,</span><span class="n" style="color: #333;">nadapter</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">tot_reads</span><span class="p">),</span><span class="n" style="color: #333;">adapter</span><span class="p">))</span></span>
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1193
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<td class="new_line diff-line-num old" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1193" class="line" lang="python"> <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;">"# misprimed_reads: %s reads (%0.1f%%) contain Himar1 prefix but don't end in TGTTA</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;">misprimed</span><span class="p">,</span><span class="n" style="color: #333;">misprimed</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">tot_reads</span><span class="p">)))</span></span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="python"> <span class="n" style="color: #333;">primer</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTAGAGGGCCCAATTCGCCCTATAGTGAGT"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="python"> <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTAGACCGTCCAGTCTGGCAGGCCGGAAAC"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="python"> <span class="n" style="color: #333;">adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GATCGGAAGAGCACACGTCTGAACTCCAGTCAC"</span></span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="python"> <span class="n" style="color: #333;">ADAPTER2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TACCACGACCA"</span> <span class="c1" style="color: #998; font-style: italic;"># rc of const2 region of R2, between barcode and genomic; these reads will be truncated here</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="python"> <span class="n" style="color: #333;">Himar1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACTTATCAGCCAACCTGTTA"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_reads</span><span class="p">,</span><span class="n" style="color: #333;">nprimer</span><span class="p">,</span><span class="n" style="color: #333;">nvector</span><span class="p">,</span><span class="n" style="color: #333;">nadapter</span><span class="p">,</span><span class="n" style="color: #333;">misprimed</span><span class="p">,</span><span class="n" style="color: #333;">ntruncated</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" 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="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">trimmed1</span><span class="p">):</span></span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'>'</span><span class="p">:</span> <span class="n" style="color: #333;">trimmed_reads</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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1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">primer</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">nprimer</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vector</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">nvector</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">nadapter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if "TGTTA" in line and Himar1 not in line: misprimed += 1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># basically, these should correspond to insertions at non-TA sites (so the terminal TA of ...TGTTA will be different)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Himar1</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Himar1</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;">line</span><span class="p">:</span> <span class="n" style="color: #333;">misprimed</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span> </span>
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1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="python"></span>
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1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="python"> <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;">"# Break-down of total reads (%s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tot_reads</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="python"> <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 reads (%0.1f%%) lack the expected Tn prefix</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;">tot_reads</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">tot_tgtta</span><span class="p">,(</span><span class="n" style="color: #333;">tot_reads</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">tot_tgtta</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">tot_reads</span><span class="p">)))</span></span>
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1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="python"></span>
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1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="python"> <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;">"# Break-down of trimmed reads with valid Tn prefix (%s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">trimmed_reads</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="python"> <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;">"# primer_matches: %s reads (%0.1f%%) contain %s (Himar1)</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;">nprimer</span><span class="p">,</span><span class="n" style="color: #333;">nprimer</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">trimmed_reads</span><span class="p">),</span><span class="n" style="color: #333;">primer</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="python"> <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;">"# vector_matches: %s reads (%0.1f%%) contain %s (phiMycoMarT7)</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;">nvector</span><span class="p">,</span><span class="n" style="color: #333;">nvector</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">trimmed_reads</span><span class="p">),</span><span class="n" style="color: #333;">vector</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="python"> <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;">"# adapter_matches: %s reads (%0.1f%%) contain %s (Illumina/TruSeq index)</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;">nadapter</span><span class="p">,</span><span class="n" style="color: #333;">nadapter</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">trimmed_reads</span><span class="p">),</span><span class="n" style="color: #333;">adapter</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="python"> <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;">"# misprimed_reads: %s reads (%0.1f%%) contain Himar1 prefix but don't end in TGTTA</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;">misprimed</span><span class="p">,</span><span class="n" style="color: #333;">misprimed</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</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;">trimmed_reads</span><span class="p">)))</span></span>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="python"></span>
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1194
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="python"> <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;">"# read_length: %s bp</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">read_length</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="python"> <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_R1_genomic_length: %0.1f bp</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">mean_r1_genomic</span><span class="p">)</span></span>
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1196
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1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">single_end</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;">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_R2_genomic_length: %0.1f bp</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">mean_r2_genomic</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#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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3
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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">2</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">3</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[TRANSIT]"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#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">@@ -34,9 +34,9 @@ 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;"><span class="idiff left right">ignor</span>ed_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 class="n" style="color: #333;">refs</span><span class="o" style="font-weight: 600;">=</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;"><span class="idiff left right">exclud</span>ed_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 class="n" style="color: #333;">refs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]):</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;"><span class="idiff left">ignor</span>ed_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff right">ignor</span>ed_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="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;"><span class="idiff left">exclud</span>ed_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff right">exclud</span>ed_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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,18 +61,18 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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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;"><span class="idiff left">ignor</span>ed_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;">"-<span class="idiff right">ignor</span>e-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="LC64" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">exclud</span>ed_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;">"-<span class="idiff right">exclud</span>e-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="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 --<span class="idiff left right">ignor</span>e-conditions --include-conditions -iN -iC -PC --ref"</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 --<span class="idiff left right">exclud</span>e-conditions --include-conditions -iN -iC -PC --ref"</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="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;"><span class="idiff left right">ignor</span>ed_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 class="n" style="color: #333;">refs</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;"><span class="idiff left right">exclud</span>ed_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 class="n" style="color: #333;">refs</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,8 +195,20 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">conditionsByFile</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">filenamesInCombWig</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">conditionsList</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;">select_conditions</span><span class="p">(</span><span class="n" style="color: #333;">conditions</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_conditions</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span><span class="n" style="color: #333;">orderingMetadata</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</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;">filter_wigs_by_conditions2</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">conditionsList</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">conditionsList</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;">select_conditions</span><span class="p">(</span><span class="n" style="color: #333;">conditions</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_conditions</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">excluded_conditions</span><span class="p">,</span><span class="n" style="color: #333;">orderingMetadata</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#data, conditions, _, _ = self.filter_wigs_by_conditions2(data, conditions, conditionsList)</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">metadata</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;">get_samples_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">conditionNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'Condition'</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># original Condition names for each sample, as ordered list </span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">fileNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'Filename'</span><span class="p">]</span> </span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">fileNames</span><span class="p">,</span> <span class="n" style="color: #333;">conditionNames</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</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;">filter_wigs_by_conditions3</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">fileNames</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">conditionNames</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># original Condition column in samples metadata file</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_conditions</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">excluded_conditions</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conditionNames</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># this is kind of redundant for ANOVA, but it is here because condition, covars, and interactions could have been manipulated for ZINB</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="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;">read_genes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC214" 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">@@ -238,7 +250,7 @@ class AnovaMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;"> Optional Arguments:</span></span>
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<pre style="margin: 0;"> <span id="LC251" 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="LC252" 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;"> --<span class="idiff left">ignor</span>e-conditions <cond1,...> := Comma-separated list of conditions to <span class="idiff right">ignor</span>e (Default: none)</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"><span class="s" style="color: #d14;"> --<span class="idiff left">exclud</span>e-conditions <cond1,...> := Comma-separated list of conditions to <span class="idiff right">exclud</span>e (Default: none)</span></span>
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<pre style="margin: 0;"> <span id="LC254" 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="LC255" 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="LC256" 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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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#a067391127fae50dcf63c3968bd732956357ed52"><strong>src/pytransit/analysis/base.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">@@ -509,7 +509,7 @@ class MultiConditionMethod(AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"><span class="s" style="color: #d14;"> Class to be inherited by analysis methods that compare essentiality between multiple conditions (e.g Anova).</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC512" 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;">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_path</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">LOESS</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">ignoreCodon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ignor</span>ed_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>
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<pre style="margin: 0;">+<span id="LC512" 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;">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_path</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">LOESS</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">ignoreCodon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">exclud</span>ed_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>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">AnalysisMethod</span><span class="p">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">short_name</span><span class="p">,</span> <span class="n" style="color: #333;">long_name</span><span class="p">,</span> <span class="n" style="color: #333;">short_desc</span><span class="p">,</span> <span class="n" style="color: #333;">long_desc</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">annotation_path</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">combined_wig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combined_wig</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -518,24 +518,24 @@ class MultiConditionMethod(AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">NTerminus</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nterm</span></span>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">CTerminus</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cterm</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">unknown_cond_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FLAG-UNMAPPED-CONDITION-IN-WIG"</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ignor</span>ed_conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff right">ignor</span>ed_conditions</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">exclud</span>ed_conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff right">exclud</span>ed_conditions</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">included_conditions</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_wigs_by_conditions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">covariates</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;"><span class="idiff left right">ignor</span>ed_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>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_wigs_by_conditions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">covariates</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;"><span class="idiff left right">exclud</span>ed_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>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"><span class="s" style="color: #d14;"> Filters conditions that are <span class="idiff left right">ignor</span>ed/included.</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"><span class="s" style="color: #d14;"> Filters conditions that are <span class="idiff left right">exclud</span>ed/included.</span></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"><span class="s" style="color: #d14;"> ([[Wigdata]], [Condition], [[Covar]], [Condition], [Condition]) -> Tuple([[Wigdata]], [Condition])</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">ignor</span>ed_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="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right">ignor</span>ed_conditions</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">included_conditions</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">exclud</span>ed_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="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right">exclud</span>ed_conditions</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">included_conditions</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python"> <span class="n" style="color: #333;">d_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">cond_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">filtered_indexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[];</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC532" 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;"><span class="idiff left right">ignor</span>ed_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">included_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC533" 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;">"Both <span class="idiff left right">ignor</span>ed and included conditions have len > 0"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC532" 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;"><span class="idiff left right">exclud</span>ed_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">included_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC533" 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;">"Both <span class="idiff left right">exclud</span>ed and included conditions have len > 0"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC534" 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="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ignor</span>ed_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC536" 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;">"conditions <span class="idiff left">ignor</span>ed: {0}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right">ignor</span>ed_conditions</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">exclud</span>ed_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC536" 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;">"conditions <span class="idiff left">exclud</span>ed: {0}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right">exclud</span>ed_conditions</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC537" 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;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">conditions</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</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;">unknown_cond_flag</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">c</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;"><span class="idiff left right">ignor</span>ed_conditions</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</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;">unknown_cond_flag</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">c</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;"><span class="idiff left right">exclud</span>ed_conditions</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">d_filtered</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">cond_filtered</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">conditions</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="LC541" class="line" lang="python"> <span class="n" style="color: #333;">filtered_indexes</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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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">@@ -565,19 +565,19 @@ class MultiConditionMethod(AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># input: conditions are per wig; orderingMetdata comes from tnseq_tools.read_samples_metadata()</span></span>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># output: conditionsList is selected subset of conditions (unique, in preferred order)</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">select_conditions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">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;"><span class="idiff left right">ignor</span>ed_conditions</span><span class="p">,</span><span class="n" style="color: #333;">orderingMetadata</span><span class="p">):</span> </span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">select_conditions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">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;"><span class="idiff left right">exclud</span>ed_conditions</span><span class="p">,</span><span class="n" style="color: #333;">orderingMetadata</span><span class="p">):</span> </span>
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<pre style="margin: 0;"> <span id="LC569" 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;">included_conditions</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;">conditionsList</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">included_conditions</span></span>
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<pre style="margin: 0;"> <span id="LC570" 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="LC571" class="line" lang="python"> <span class="n" style="color: #333;">conditionsList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <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;">orderingMetadata</span><span class="p">[</span><span class="s" style="color: #d14;">'condition'</span><span class="p">]:</span> <span class="c1" style="color: #998; font-style: italic;"># the order conds appear in metadata file, duplicated for each sample</span></span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</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;">conditionsList</span><span class="p">:</span> <span class="n" style="color: #333;">conditionsList</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="python"> <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;"><span class="idiff left right">ignor</span>ed_conditions</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <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;"><span class="idiff left right">exclud</span>ed_conditions</span><span class="p">:</span> </span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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 class="n" style="color: #333;">conditionsList</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">conditionsList</span></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_wigs_by_conditions2</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">conditionsList</span><span class="p">,</span> <span class="n" style="color: #333;">covariates</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>
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"><span class="s" style="color: #d14;"> Filters conditions that are <span class="idiff left right">ignor</span>ed/included.</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"><span class="s" style="color: #d14;"> Filters conditions that are <span class="idiff left right">exclud</span>ed/included.</span></span>
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python"><span class="s" style="color: #d14;"> ([[Wigdata]], [Condition], [[Covar]], [Condition], [Condition]) -> Tuple([[Wigdata]], [Condition])</span></span>
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">d_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">cond_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">filtered_indexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="p">[],</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">@@ -596,7 +596,48 @@ class MultiConditionMethod(AnalysisMethod):</td>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python"> <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;">covariates_filtered</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"> <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;">interactions_filtered</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC599" 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="LC599" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_wigs_by_conditions3</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">fileNames</span><span class="p">,</span> <span class="n" style="color: #333;">conditionNames</span><span class="p">,</span> <span class="n" style="color: #333;">included_cond</span><span class="p">,</span> <span class="n" style="color: #333;">excluded_cond</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">covariates</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>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"><span class="s" style="color: #d14;"> Filters conditions that are excluded/included; also extract cond, covar, and interaction labels</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"><span class="s" style="color: #d14;"> conditionNames: based on original Conditions column in metadata</span></span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"><span class="s" style="color: #d14;"> conditions: user might have specified an alternative column to analyze (list of labels parallel to wigs)</span></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">fileNames_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">condNames_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">d_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">cond_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">filtered_indexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC608" 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;">included_cond</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">conditionNames</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">included_cond</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">conditionNames</span><span class="p">[</span><span class="n" style="color: #333;">i</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="n" style="color: #333;">excluded_cond</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">d_filtered</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">fileNames_filtered</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">fileNames</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="LC611" class="line" lang="python"> <span class="n" style="color: #333;">condNames_filtered</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">conditionNames</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="LC612" class="line" lang="python"> <span class="n" style="color: #333;">cond_filtered</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">conditions</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="LC613" class="line" lang="python"> <span class="n" style="color: #333;">filtered_indexes</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"> <span class="n" style="color: #333;">covariates_filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filtered_indexes</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;">covariates</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"> <span class="n" style="color: #333;">interactions_filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filtered_indexes</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;">interactions</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</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;">d_filtered</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;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">fileNames_filtered</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;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">condNames_filtered</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">cond_filtered</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">covariates_filtered</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">interactions_filtered</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return a hash table of parallel lists, indexed by column header</span></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_samples_metadata</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="LC627" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">):</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" 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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631
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<pre style="margin: 0;">+<span id="LC631" 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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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header</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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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header</span><span class="p">:</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">)):</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">header</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">i</span><span class="p">])</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#######################3</span></span>
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641
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TransitAnalysis</span><span class="p">:</span></span>
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643
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<pre style="margin: 0;"> <span id="LC643" 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;">sn</span><span class="p">,</span> <span class="n" style="color: #333;">ln</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;">tn</span><span class="p">,</span> <span class="n" style="color: #333;">method_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AnalysisMethod</span><span class="p">,</span> <span class="n" style="color: #333;">gui_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AnalysisGUI</span><span class="p">,</span> <span class="n" style="color: #333;">filetypes</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">TransitFile</span><span class="p">]):</span></span>
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<li id="a522d0d990a6ccfbb24eba81a727b32c79e5f81a">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#a522d0d990a6ccfbb24eba81a727b32c79e5f81a"><strong>src/pytransit/analysis/gumbel.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="333" style="width: 35px; color: rgba(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="333" style="width: 35px; color: rgba(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">@@ -333,6 +333,9 @@ class GumbelMethod(base.SingleConditionMethod):</td>
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333
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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;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Getting Data"</span><span class="p">)</span></span>
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334
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334
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<pre style="margin: 0;"> <span id="LC334" 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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335
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">K</span><span class="p">,</span><span class="n" style="color: #333;">N</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">shape</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span><span class="n" style="color: #333;">axis</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="LC337" class="line" lang="python"> <span class="n" style="color: #333;">nsites</span><span class="p">,</span><span class="n" style="color: #333;">nzeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># perhaps I should say >minCount</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">sat</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nsites</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nzeros</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;">nsites</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC340" 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;">normalization</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">normalization</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"nonorm"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC341" 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;">"Normalizing using: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">normalization</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -412,13 +415,14 @@ class GumbelMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">phi_old</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phi_new</span></span>
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<pre style="margin: 0;"> <span id="LC417" 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="LC415" 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 Gumbel Method... %5.1f%%"</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="p">(</span><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 class="p">)</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;">samples</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;">burnin</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC418" 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 Gumbel Method<span class="idiff left right"> with Binomial Essentiality Calls</span>... %5.1f%%"</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="p">(</span><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 class="p">)</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;">samples</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;">burnin</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC419" 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="LC420" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">ZBAR</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;">apply_along_axis</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">Z_sample</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">ess_t</span><span class="p">,</span> <span class="n" style="color: #333;">non_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat_tools</span><span class="p">.</span><span class="n" style="color: #333;">bayesian_ess_thresholds</span><span class="p">(</span><span class="n" style="color: #333;">ZBAR</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">binomial_n</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;">log10</span><span class="p">(</span><span class="mf" style="color: #099;">0.05</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;">log10</span><span class="p">(</span><span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">global_phi</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Orf k n r s zbar</span></span>
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<pre style="margin: 0;"> <span id="LC427" 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;">"#Gumbel</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC428" 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;">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">@@ -432,16 +436,20 @@ class GumbelMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC437" 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;">"#Data: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ctrldata</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)))</span> </span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Annotation path: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))</span> </span>
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<pre style="margin: 0;">-<span id="LC435" 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;">"#FDR Corrected thresholds: %f, %f</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;">ess_t</span><span class="p">,</span> <span class="n" style="color: #333;">non_t</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC436" 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;">"#MH Acceptance-Rate:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%2.2f%%</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="mf" style="color: #099;">100.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">acctot</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">count</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC439" 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;">"#Trimming of TAs near termini: N-term=%s, C-term=%s (fraction of ORF length)</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;">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 class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC440" 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;">"#Significance thresholds (FDR-corrected): Essential if Zbar>%f, Non-essential if Zbar<%f</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;">ess_t</span><span class="p">,</span> <span class="n" style="color: #333;">non_t</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC441" 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;">"#Metropolis-Hastings Acceptance-Rate:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%2.2f%%</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="mf" style="color: #099;">100.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">acctot</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">count</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC442" 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;">"#Total Iterations Performed:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%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="n" style="color: #333;">count</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC443" 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;">"#Sample Size:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%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="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC439" 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;">"#phi estimate:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">average</span><span class="p">(</span><span class="n" style="color: #333;">phi_sample</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Time: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start_time</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC441" 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="LC444" 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;">"#Total number of TA sites: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">nsites</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC445" 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;">"#Genome-wide saturation: %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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sat</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="p">)))</span> <span class="c1" style="color: #998; font-style: italic;"># datasets merged</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" 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;">"#phi estimate:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f (non-insertion probability in non-essential regions)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">average</span><span class="p">(</span><span class="n" style="color: #333;">phi_sample</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC447" 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 number of TA sites with 0 insertions to be classified as essential by Binomial: </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%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="n" style="color: #333;">binomial_n</span><span class="p">)</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Time: %s 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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start_time</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">i</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="LC443" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">G</span></span><span class="p">:</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">calls</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]<span class="idiff right">,[]</span></span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left">j</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff">enumerate</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">G</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">good_orf</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">zbar</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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">@@ -449,18 +457,30 @@ class GumbelMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">zbar</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ess_t</span><span class="p">:</span></span>
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459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"E"</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">local_sites</span><span class="p">()[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">binomial_n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">G</span><span class="p">.</span><span class="n" style="color: #333;">local_thetas</span><span class="p">()[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="mf" style="color: #099;">0.0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"EB"</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">non_t</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">zbar</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ess_t</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"U"</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">zbar</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">non_t</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NE"</span></span>
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<pre style="margin: 0;"> <span id="LC466" 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="LC467" class="line" lang="python"> <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"S"</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC469" 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="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">orf</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">desc</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">zbar</span><span class="p">,</span> <span class="n" style="color: #333;">call</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">calls</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">call</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC471" 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>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC473" 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;">"#Summary of Essentiality Calls:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC474" 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;">"# E = %4s (essential based on Gumbel)</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;">calls</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"E"</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC475" 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;">"# EB = %4s (essential based on Binomial)</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;">calls</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"EB"</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# NE = %4s (non-essential)</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;">calls</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"NE"</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC477" 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;">"# U = %4s (uncertain)</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;">calls</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"U"</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC478" 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 = %4s (too short)</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;">calls</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"S"</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC480" 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="LC481" 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="n" style="color: #333;">data</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC482" 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="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC484" 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><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Printing empty line to flush stdout </span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">transit_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Adding File: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">add_file</span><span class="p">(</span><span class="n" style="color: #333;">filetype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Gumbel"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="494" style="width: 35px; color: rgba(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">@@ -494,8 +514,9 @@ class GumbelMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">BetaGamma</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">B</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;">getGamma</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC515" 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="n" style="color: #333;">EXACT</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># estimate more accurately based on expected run len, using exact calc for small genes</span></span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">exprun</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;">ExpectedRuns_cached</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exprun</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">BetaGamma</span> <span class="c1" style="color: #998; font-style: italic;"># u is mu of Gumbel (mean=mu+gamma*beta); matching of moments</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"> <span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">gumbel_r</span><span class="p">.</span><span class="n" style="color: #333;">logcdf</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span><span class="n" style="color: #333;">u</span><span class="p">,</span><span class="n" style="color: #333;">B</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exprun</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">BetaGamma</span> <span class="c1" style="color: #998; font-style: italic;"># u is mu of Gumbel (mean=mu+gamma*beta); matching of moments </span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</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;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">gumbel_r</span><span class="p">.</span><span class="n" style="color: #333;">logcdf</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span><span class="n" style="color: #333;">u</span><span class="p">,</span><span class="n" style="color: #333;">B</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pval</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.05</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</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="LC521" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span><span class="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="LC522" 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">@@ -519,7 +540,7 @@ class GumbelMethod(base.SingleConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="p">)):</span> <span class="c1" style="color: #998; font-style: italic;"># estimate more accurately based on expected run len, using exact calc for small genes</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">EXACT</span><span class="p">:</span> <span class="n" style="color: #333;">mu</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ExpectedRuns_cached</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">BetaGamma</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">sigma</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">h0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left right">sci</span>py</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">gumbel_r</span><span class="p">.</span><span class="n" style="color: #333;">logpdf</span><span class="p">(</span><span class="n" style="color: #333;">R</span><span class="p">,</span><span class="n" style="color: #333;">mu</span><span class="p">,</span><span class="n" style="color: #333;">sigma</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">norm</span><span class="p">.</span><span class="n" style="color: #333;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">mu_s</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="n" style="color: #333;">sigma_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">w1</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;">h0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left right">num</span>py</span><span class="p">.</span><span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">gumbel_r</span><span class="p">.</span><span class="n" style="color: #333;">logpdf</span><span class="p">(</span><span class="n" style="color: #333;">R</span><span class="p">,</span><span class="n" style="color: #333;">mu</span><span class="p">,</span><span class="n" style="color: #333;">sigma</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scipy</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">norm</span><span class="p">.</span><span class="n" style="color: #333;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">mu_s</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="n" style="color: #333;">sigma_s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">w1</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SIG</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">w1</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1e-10</span><span class="p">;</span> <span class="n" style="color: #333;">h0</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1e-10</span> <span class="c1" style="color: #998; font-style: italic;"># to prevent div-by-zero; if neither class is probable, p(z1) should be ~0.5</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"> <span class="n" style="color: #333;">p_z1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">h0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">h1</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#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">@@ -48,9 +48,9 @@ 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;"><span class="idiff left right">ignor</span>ed_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 class="n" style="color: #333;">refs</span><span class="o" style="font-weight: 600;">=</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;"><span class="idiff left right">exclud</span>ed_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 class="n" style="color: #333;">refs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]):</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;"><span class="idiff left">ignor</span>ed_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff right">ignor</span>ed_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="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;"><span class="idiff left">exclud</span>ed_conditions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff right">exclud</span>ed_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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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">covars</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covars</span></span>
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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" style="width: 35px; color: rgba(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">@@ -96,18 +96,18 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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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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<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;"><span class="idiff left">ignor</span>ed_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;">"-<span class="idiff right">ignor</span>e-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="LC99" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">exclud</span>ed_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;">"-<span class="idiff right">exclud</span>e-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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<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="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 --<span class="idiff left right">ignor</span>e-conditions --include-conditions -iN -iC -PC --condition --covars --interactions --gene --ref"</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 --<span class="idiff left right">exclud</span>e-conditions --include-conditions -iN -iC -PC --condition --covars --interactions --gene --ref"</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="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;"><span class="idiff left right">ignor</span>ed_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 class="n" style="color: #333;">refs</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;"><span class="idiff left right">exclud</span>ed_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 class="n" style="color: #333;">refs</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">@@ -523,6 +523,8 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">condition_name</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;">condition</span></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if a covar is not found, this crashes; check for it?</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read it first with no condition specified, to get original Condition names</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python"> <span class="n" style="color: #333;">conditionsByFile1</span><span class="p">,</span> <span class="n" style="color: #333;">covariatesByFileList1</span><span class="p">,</span> <span class="n" style="color: #333;">interactionsByFileList1</span><span class="p">,</span> <span class="n" style="color: #333;">orderingMetadata1</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;">read_samples_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">covars</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">interactions</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># without specifiying condition</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"> <span class="n" style="color: #333;">conditionsByFile</span><span class="p">,</span> <span class="n" style="color: #333;">covariatesByFileList</span><span class="p">,</span> <span class="n" style="color: #333;">interactionsByFileList</span><span class="p">,</span> <span class="n" style="color: #333;">orderingMetadata</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;">read_samples_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">covars</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">interactions</span><span class="p">,</span> <span class="n" style="color: #333;">condition_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">condition_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">## [Condition] in the order of files in combined wig</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">@@ -538,19 +540,37 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">interactionsByFileList</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">filenamesInCombWig</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">conditionsList</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;">select_conditions</span><span class="p">(</span><span class="n" style="color: #333;">conditions</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_conditions</span><span class="p">,</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ignored_conditions</span><span class="p">,</span><span class="n" style="color: #333;">orderingMetadata</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">covariates</span><span class="p">,</span> <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filter_wigs_by_conditions2</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this was the old way to filter samples, where --include/exclude-conditions depended on which --condition was specified</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#conditionsList = self.select_conditions(conditions,self.included_conditions,self.excluded_conditions,orderingMetadata)</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#data, conditions, covariates, interactions = self.filter_wigs_by_conditions2(</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># data,</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># conditions,</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># conditionsList,</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># covariates = covariates,</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># interactions = interactions)</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#filesByCondition = self.invertDict(conditionsByFile)</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#samples_used = set()</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#for cond in conditionsList: samples_used.update(filesByCondition[cond])</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="n" style="color: #333;">metadata</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;">get_samples_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">conditionNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'Condition'</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># original Condition names for each sample, as ordered list </span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">fileNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">'Filename'</span><span class="p">]</span> </span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this is the new way to filter samples, where --include/exclude-conditions refers to Condition column in metadata, regardless of whether --condition was specified</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">fileNames</span><span class="p">,</span> <span class="n" style="color: #333;">conditionNames</span><span class="p">,</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="n" style="color: #333;">covariates</span><span class="p">,</span> <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filter_wigs_by_conditions3</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">conditions</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">conditionsList</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">fileNames</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"> <span class="n" style="color: #333;">conditionNames</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># original Condition column in samples metadata file</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_conditions</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">excluded_conditions</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="n" style="color: #333;">conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conditions</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># user might have specified a column other than Condition</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">covariates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covariates</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <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 class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">conditionsList</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;">set</span><span class="p">(</span><span class="n" style="color: #333;">conditions</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># unique condition labels, filtered</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">samples_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">fileNames</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># show the samples associated with each condition (and covariates or interactions, if defined), and count samples in each cross-product of vars</span></span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="n" style="color: #333;">filesByCondition</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;">invertDict</span><span class="p">(</span><span class="n" style="color: #333;">conditionsByFile</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">samples_used</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cond</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">conditionsList</span><span class="p">:</span> <span class="n" style="color: #333;">samples_used</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">filesByCondition</span><span class="p">[</span><span class="n" style="color: #333;">cond</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="nb" style="color: #0086b3;">vars</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">condition_name</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">covars</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;">interactions</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">vars2vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">vars2vals</span><span class="p">[</span><span class="n" style="color: #333;">condition_name</span><span class="p">]</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;">set</span><span class="p">(</span><span class="n" style="color: #333;">conditions</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">@@ -558,7 +578,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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558
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578
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<pre style="margin: 0;"> <span id="LC578" 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;">var</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">interactions</span><span class="p">):</span> <span class="n" style="color: #333;">vars2vals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">]</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;">set</span><span class="p">(</span><span class="n" style="color: #333;">interactions</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>
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559
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">varsByFileList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">conditionsByFile</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">covariatesByFileList</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">interactionsByFileList</span></span>
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580
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<pre style="margin: 0;"> <span id="LC580" 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;">var</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Condition/Covariate/Interaction: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" 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;">\n</span><span class="s" style="color: #d14;"><span class="idiff left right">samples for </span>Condition/Covariate/Interaction: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"> <span class="n" style="color: #333;">filesByVar</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;">invertDict</span><span class="p">(</span><span class="n" style="color: #333;">varsByFileList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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563
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583
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<pre style="margin: 0;"> <span id="LC583" 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;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filesByVar</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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564
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">samples_used</span><span class="p">.</span><span class="n" style="color: #333;">intersection</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)))</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="604" style="width: 35px; color: rgba(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">@@ -584,7 +604,11 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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584
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ic1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">ic1</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ic1</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;">else</span> <span class="p">(</span><span class="n" style="color: #333;">ic1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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585
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">c2</span><span class="p">,</span> <span class="n" style="color: #333;">i2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ic2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">ic2</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ic2</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;">else</span> <span class="p">(</span><span class="n" style="color: #333;">ic2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC587" 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;">included_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># use --include-conditions to determine order of columns in output file</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this only works if an alternative --condition was not specified</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># otherwise don't try to order them this way because it gets too complicated</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># possibly should require --covars and --interactions to be unspecified too</span></span>
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<pre style="margin: 0;">+<span id="LC611" 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;">condition</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Condition"</span> <span class="ow" style="font-weight: 600;">and</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;">included_conditions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</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;">excluded_conditions</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">condDiff</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;">included_conditions</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">c1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_conditions</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">c2</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">## Order by interaction, if stat belongs to same condition</span></span>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">condDiff</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</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">@@ -640,8 +664,8 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python"><span class="s" style="color: #d14;"> Optional Arguments:</span></span>
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<pre style="margin: 0;"> <span id="LC666" 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;"> --<span class="idiff left">ignor</span>e-conditions <cond1,cond2> := Comma separated list of conditions to <span class="idiff right">ignor</span>e, 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 <span class="idiff left right">ignor</span>ed.</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"><span class="s" style="color: #d14;"> --<span class="idiff left">exclud</span>e-conditions <cond1,cond2> := Comma separated list of conditions to <span class="idiff right">exclud</span>e, for the analysis.</span></span>
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<pre style="margin: 0;">+<span id="LC668" 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 <span class="idiff left right">exclud</span>ed.</span></span>
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<pre style="margin: 0;"> <span id="LC669" 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="LC670" 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="LC671" 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="LC1" class="line" lang="plaintext">Id <span class="idiff left">New</span>Condition<span class="idiff right">Col</span> Filename Batch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">c1 Cholesterol src/pytransit/data/cholesterol_H37Rv_rep1.wig b1</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">c2 Cholesterol src/pytransit/data/cholesterol_H37Rv_rep2.wig b1</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">c3 Cholesterol src/pytransit/data/cholesterol_H37Rv_rep3.wig b2</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">g1 Glycerol src/pytransit/data/glycerol_H37Rv_rep1.wig b2</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">g2 Glycerol src/pytransit/data/glycerol_H37Rv_rep2.wig b2</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Id Condition Filename Batch<span class="idiff left right"> NewConditionCol</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">c1 Cholesterol src/pytransit/data/cholesterol_H37Rv_rep1.wig b1<span class="idiff left right"> X</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">c2 Cholesterol src/pytransit/data/cholesterol_H37Rv_rep2.wig b1<span class="idiff left right"> X</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">c3 Cholesterol src/pytransit/data/cholesterol_H37Rv_rep3.wig b2<span class="idiff left right"> X</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">g1 Glycerol src/pytransit/data/glycerol_H37Rv_rep1.wig b2<span class="idiff left right"> Y</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">g2 Glycerol src/pytransit/data/glycerol_H37Rv_rep2.wig b2<span class="idiff left right"> Y</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,18 +32,69 @@ probability of this using a Bayesian model.</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">How does it work?</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">-----------------</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">| <span class="idiff left right">For a formal description of how this method works, see our paper [DeJesus2013]_:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">| </span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">| DeJesus, M.A., Zhang, Y.J., Sassettti, C.M., Rubin, E.J.,</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> Sacchettini, J.C., and Ioerger, T.R. (2013).</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">| `Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. <http://www.ncbi.nlm.nih.gov/pubmed/23361328>`_ *Bioinformatics*, 29(6):695-703.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">This method for identifying essential genes is based on analyzing</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">'gaps', or consecutive sequences of TA sites lacking insertions.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">The statistical significance of the length of a gap is determined</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">using the Gumbel distribution, which is a form of an Extreme-Value distribution.</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Example</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">-------</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">For a formal description of how this method works, see our paper [DeJesus2013]_:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">| </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> DeJesus, M.A., Zhang, Y.J., Sassettti, C.M., Rubin, E.J.,</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> Sacchettini, J.C., and Ioerger, T.R. (2013). `Bayesian analysis of</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> gene essentiality based on sequencing of transposon insertion</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> libraries. <http://www.ncbi.nlm.nih.gov/pubmed/23361328>`_</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> *Bioinformatics*, 29(6):695-703.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">**Update (2021) - Binomial** </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Since the Gumbel method depends on the overall</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">saturation (percent of TA sites with insertions), it can sometimes</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">call a lot of smaller genes 'Uncertain'. This might reduce the total</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">number of essentials detected. For example, if the saturation is</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">~30%, no genes with fewer than ~10 TA sites might confidently be</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">labeled as Essential. In particular, there are often genes with no</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">insertions that look like they should obviously be called essential,</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">and yet, they are too short to be confidently called essential in</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">low-saturation datasets by the conservative Gumbel model.</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">To compensate for this, we have added a simple **Binomial** model for</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">detecting small genes totally lacking insertions (described in `(Choudhery et al, 2021)</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"><https://www.biorxiv.org/content/10.1101/2021.07.01.450749v2>`_). In</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">the output file, they are labled as 'EB' to distinguish them from</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">essentials (E) based on the Gumbel model. The EB genes supplement</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">genes marked E by Gumbel, and the combination of the 2 groups (E and</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">EB) should be considered as 'essentials'. The number of genes in</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">each category is reported in a table in the header of the output file, like this:</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> python3 transit.py gumbel <comma-separated .wig files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> (for an M. tuberculosis TnSeq dataset with 60% saturation:)</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> #Summary of Essentiality Calls:</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> # E = 551 (essential based on Gumbel)</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> # EB = 94 (essential based on Binomial)</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> # NE = 2829 (non-essential)</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> # U = 262 (uncertain)</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> # S = 254 (too short)</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> (for an M. tuberculosis TnSeq dataset with 40% saturation:)</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> # E = 194 (essential based on Gumbel)</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> # EB = 315 (essential based on Binomial)</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> # NE = 2441 (non-essential)</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> # U = 774 (uncertain)</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> # S = 266 (too short)</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Usage</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">-----</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> > python3 transit.py gumbel <comma-separated .wig files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"> Optional Arguments:</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> -s <integer> := Number of samples. Default: -s 10000</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> -b <integer> := Number of Burn-in samples. Default -b 500</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">@@ -1053,7 +1104,7 @@ Example</td>
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1053
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="plaintext"> python3 transit.py anova <combined wig file> <samples_metadata file> <annotation .prot_table> <output file> [Optional Arguments]</span>
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1054
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="plaintext"> Optional Arguments:</span>
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1055
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1106
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="plaintext"> -n <string> := Normalization method. Default: -n TTR</span>
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1056
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<pre style="margin: 0;">-<span id="LC1056" class="line" lang="plaintext"> --<span class="idiff left right">ignor</span>e-conditions <cond1,...> := Comma separated list of conditions to ignore, for the analysis. Default: None</span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="plaintext"> --<span class="idiff left right">exclud</span>e-conditions <cond1,...> := Comma separated list of conditions to ignore, for the analysis. Default: None</span>
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1057
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="plaintext"> --include-conditions <cond1,...> := Comma separated list of conditions to include, for the analysis. Default: All</span>
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1058
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1109
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<pre style="margin: 0;"> <span id="LC1109" 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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1059
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1110
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<pre style="margin: 0;"> <span id="LC1110" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1092,7 +1143,7 @@ The following parameters are available for the ANOVA method:</td>
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1144" 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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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC1095" class="line" lang="plaintext">- **\-\-<span class="idiff left right">ignor</span>e-conditions:** Can use this to drop conditions not of interest.</span>
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="plaintext">- **\-\-<span class="idiff left right">exclud</span>e-conditions:** Can use this to drop conditions not of interest.</span>
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1148" 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="LC1149" class="line" lang="plaintext"> By default, LFCs for each gene in each condition are calculated with respect</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">@@ -1218,8 +1269,8 @@ Example</td>
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="plaintext"> python3 transit.py zinb <combined wig file> <samples_metadata file> <annotation .prot_table> <output file> [Optional Arguments]</span>
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<pre style="margin: 0;"> <span id="LC1270" class="line" lang="plaintext"> Optional Arguments:</span>
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<pre style="margin: 0;"> <span id="LC1271" class="line" lang="plaintext"> -n <string> := Normalization method. Default: -n TTR</span>
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<pre style="margin: 0;">-<span id="LC1221" class="line" lang="plaintext"> --<span class="idiff left">ignor</span>e-conditions <cond1,<span class="idiff right">cond2</span>> := Comma separated list of conditions to ignore, for the analysis. Default: None</span>
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<pre style="margin: 0;">-<span id="LC1222" class="line" lang="plaintext"> --include-conditions <cond1,<span class="idiff left right">cond2</span>> := Comma separated list of conditions to include, for the analysis. Default: All</span>
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="plaintext"> --<span class="idiff left">exclud</span>e-conditions <cond1,<span class="idiff right">...</span>> := Comma separated list of conditions to ignore, for the analysis. Default: None</span>
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="plaintext"> --include-conditions <cond1,<span class="idiff left right">...</span>> := Comma separated list of conditions to include, for the analysis. Default: All</span>
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<pre style="margin: 0;"> <span id="LC1274" 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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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="plaintext"> -iN <float> := Ignore TAs occuring within given percentage of the N terminus. Default: -iN 5</span>
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="plaintext"> -iC <float> := Ignore TAs occuring within given percentage of the C terminus. Default: -iC 5</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1281,10 +1332,10 @@ of the combined_wig (including pathnames, if present).</td>
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="plaintext">Parameters</span>
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="plaintext">----------</span>
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<pre style="margin: 0;"> <span id="LC1334" 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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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="plaintext">The following parameters are available for the <span class="idiff left right">ZINB </span>method:</span>
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1285
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<pre style="margin: 0;"> <span id="LC1336" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1337" 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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<pre style="margin: 0;">-<span id="LC1287" class="line" lang="plaintext">- **\-\-<span class="idiff left right">ignor</span>e-conditions:** Ignores the given set of conditions from the ZINB test.</span>
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="plaintext">- **\-\-<span class="idiff left right">exclud</span>e-conditions:** Ignores the given set of conditions from the ZINB test.</span>
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<pre style="margin: 0;"> <span id="LC1339" 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="LC1340" class="line" lang="plaintext">- **Normalization Method:** Determines which normalization method to</span>
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="plaintext"> use when comparing datasets. Proper normalization is important as it</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#2db304110a376933b3ccb003bd122d724bfb8159"><strong>src/pytransit/stat_tools.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -512,7 +512,7 @@ def F_shuffle_dict_libraries(*args, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC512" 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;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">permutation</span><span class="p">(</span><span class="n" style="color: #333;">combined</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("perm", perm)</span></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("perm[:n1]", perm[:n1])</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">E</span><span class="p">[</span><span class="n" style="color: #333;">L</span><span class="p">]</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;">perm</span><span class="p">[:</span><span class="n" style="color: #333;">n1</span><span class="p">],</span> <span class="n" style="color: #333;">perm</span><span class="p">[</span><span class="n" style="color: #333;">n1</span><span class="p">:]])</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">E</span><span class="p">[</span><span class="n" style="color: #333;">L</span><span class="p">]</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;">perm</span><span class="p">[:</span><span class="n" style="color: #333;">n1</span><span class="p">],</span> <span class="n" style="color: #333;">perm</span><span class="p">[</span><span class="n" style="color: #333;">n1</span><span class="p">:]]<span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">object</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("D[L]", D[L])</span></span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">E</span></span>
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<pre style="margin: 0;"> <span id="LC518" 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">@@ -566,7 +566,8 @@ def resampling(data1, data2, S=10000, testFunc=F_mean_diff_flat,</td>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># - Check library strings match in some way</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">lib_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">lib_str1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">^</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">lib_str2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lib_diff</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"At least one library string has a letter not used by the other:\ %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lib_diff</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#raise ValueError("At least one library string has a letter not used by the other:\ %s" % ", ".join(lib_diff))</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"At least one library string has a letter not used by the other: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lib_diff</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># - Check input has some data</span></span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">data1</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="s" style="color: #d14;">"Data1 cannot be empty"</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">@@ -714,7 +715,7 @@ def combine_lib_dicts(L1, L2):</td>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"> <span class="n" style="color: #333;">KEYS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">L1</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="n" style="color: #333;">DATA</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">K</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">KEYS</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"> <span class="n" style="color: #333;">DATA</span><span class="p">[</span><span class="n" style="color: #333;">K</span><span class="p">]</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;">L1</span><span class="p">[</span><span class="n" style="color: #333;">K</span><span class="p">],</span> <span class="n" style="color: #333;">L2</span><span class="p">[</span><span class="n" style="color: #333;">K</span><span class="p">]])</span></span>
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">DATA</span><span class="p">[</span><span class="n" style="color: #333;">K</span><span class="p">]</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;">L1</span><span class="p">[</span><span class="n" style="color: #333;">K</span><span class="p">],</span> <span class="n" style="color: #333;">L2</span><span class="p">[</span><span class="n" style="color: #333;">K</span><span class="p">]]<span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">object</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DATA</span></span>
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#d89b43ded7022712aee60a6466cbc62fe14a73a3"><strong>src/pytransit/tnseq_tools.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,6 +80,9 @@ def read_samples_metadata(metadata_file, covarsToRead = [], interactionsToRead =</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">interactionsByFileList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[{}</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="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;">interactionsToRead</span><span class="p">))]</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">headersToRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">condition_name</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">(),</span> <span class="s" style="color: #d14;">"filename"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">orderingMetadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">'condition'</span><span class="p">:</span> <span class="p">[],</span> <span class="s" style="color: #d14;">'interaction'</span><span class="p">:</span> <span class="p">[]</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">headersToRead</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">covarsToRead</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">interactionsToRead</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">metadata_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mfile</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mfile</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">headIndexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/fac2650606c9600626d84ca58087250253aed295#8932e01e75ea1b89ecb1e441751d55c66ddb844e"><strong>tests/test_tpp.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">@@ -35,7 +35,7 @@ NOFLAG_PRIMER = [</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"# FR_corr (Fwd templates vs. Rev templates): 0.019"</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;">"# transposon type: Himar1"</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;">"# protocol type: Sassetti"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"# primer_matches: 8 reads (0.8%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1)"</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"# <span class="idiff left right"> </span>primer_matches: 8 reads (0.8%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1)"</span></span>
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39
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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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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">MME1_PROTOCOL</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">@@ -46,7 +46,7 @@ MME1_PROTOCOL = [</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"# NZ_mean (among templates): 1.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"# transposon type: Himar1"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"# protocol type: Mme1"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"# primer_matches: 8 reads (0.8%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1)"</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"# <span class="idiff left right"> </span>primer_matches: 8 reads (0.8%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1)"</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">FLAG_PRIMER</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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