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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f">f8a1a562</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-12-11T10:15:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.9</pre>
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</ul>
<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360">
HISTORY.md
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<li class="file-stats">
<a href="#059a93c69080af2f6054c5324203b7af73cc5b83">
bcbio/bam/__init__.py
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<li class="file-stats">
<a href="#db6099147d782b81be3efa804f6a41b2a6b7ebf5">
bcbio/broad/picardrun.py
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<li class="file-stats">
<a href="#fb17eef4888c4f7198909ebc1616eb92a3fed380">
bcbio/chipseq/__init__.py
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<li class="file-stats">
<a href="#e058999dc6b36492007fce47afb7a70ca8b25e3d">
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bcbio/chipseq/atac.py
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<a href="#4eabad8cbe351e3e3d7466ee25d9d970b164368a">
bcbio/chipseq/macs2.py
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<li class="file-stats">
<a href="#fbfb96675c481efdacfedf0214b473e7d623d79c">
bcbio/chipseq/peaks.py
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<li class="file-stats">
<a href="#fee19f4f498a2b34eca43fa79376fa526f252577">
bcbio/heterogeneity/chromhacks.py
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<a href="#037a5da84cee54d04c6672861c844615a844912f">
bcbio/ngsalign/bwa.py
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<li class="file-stats">
<a href="#bbb7842f2be9690f4ae67a1de2c07f322d6e261e">
bcbio/ngsalign/star.py
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<a href="#28669a7ddccdf8ac47c577727840379bba16c871">
bcbio/pipeline/rnaseq.py
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<a href="#6a5842dd9e3c5daac8e6d62a34e4d60ab86b78bf">
bcbio/pipeline/run_info.py
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<li class="file-stats">
<a href="#fac91f905233560f253b7063f3b6889aeca3af62">
bcbio/pipeline/sample.py
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<li class="file-stats">
<a href="#0b928052acb70b506a8457627983f038aaf8fd4d">
bcbio/qc/multiqc.py
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<li class="file-stats">
<a href="#1632995720dec2c83890f793045a09678042e862">
bcbio/qc/viral.py
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<li class="file-stats">
<a href="#953a5484c194dec73486a5e85ad272cd898cbf31">
bcbio/upload/__init__.py
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<li class="file-stats">
<a href="#b5f97c2465c41ae9654e19860697f479dc1cf205">
bcbio/variation/effects.py
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<li class="file-stats">
<a href="#f1753c26ad7dd9c07a75161a266af4cb354610d3">
docs/contents/configuration.rst
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<a href="#46caee1d50ca05a5fb7d450ccc1f3934ae0c9bc3">
docs/contents/internals.rst
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<a href="#25f1fbed65859fbfcdb276507ddb9f56ebb11056">
docs/contents/outputs.rst
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<li class="file-stats">
<a href="#b1655f936472b3a6a6a310218f78e1d19987454b">
requirements-conda.txt
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<li class="file-stats">
<a href="#bacc76312ae1e30f71298a0e5abf86c8e5dbec70">
scripts/bcbio_setup_genome.py
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<a href="#c493fa11b32390866834a9938a57d281ac430b70">
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tests/data/atac/atac_1.fq
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tests/data/atac/atac_2.fq
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tests/data/automated/run_info-atacseq.yaml
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<li class="file-stats">
<a href="#b2ff7250c9f6e5d3abe1718225f05b9c670270b2">
tests/data/automated/run_info-chipseq.yaml
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<li class="file-stats">
<a href="#2e946528151ae7bd001de04d59a142da8ee2df0c">
tests/integration/test_automated_analysis.py
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<li class="file-stats">
<a href="#638319436d10230518a06abc53d6225665c74c4e">
tests/pytest.ini
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<h4>Changes:</h4>
<li id="d30b04166486087de34ff05cf278d3dd2ddd2360">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#d30b04166486087de34ff05cf278d3dd2ddd2360"><strong>HISTORY.md</strong></a>
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1
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.1.8</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.1.9 (in progress)</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">-</span> Fix for get VEP cache.</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">-</span> Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY).</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">-</span> Remove mitochondrial reads from ChIP/ATAC-seq calling.</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">-</span> Add documentation describing ATAC-seq outputs.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">-</span> Add ENCODE library complexity metrics for ATAC/ChIP-seq to MultiQC report </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"> (see https://www.encodeproject.org/data-standards/terms/#library for a description of the metrics)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">-</span> Add STAR sample-specific 2-pass. This helps assign a moderate number of reads per genes. Thanks</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"> to @naumenko-sa for the intial implementation and push to get this going.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">-</span> Index transcriptomes only once for pseudo/quasi aligner tools. This fixes race conditions that</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"> can happen.</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">-</span> Add --buildversion option, for tracking which version of a gene build was used. This is used</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"> during <span class="sb" style="color: #d14;">`bcbio_setup_genome.py`</span>. Suggested formats are source_version, so Ensembl_94, </span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"> EnsemblMetazoa_25, FlyBase_26, etc.</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">-</span> Sort MACS2 bedgraph files before compressing. Thanks to @LMannarino for the suggestion.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">-</span> Check for the reserved field <span class="sb" style="color: #d14;">`sample`</span> in RNA-seq metadata and quit with a useful error message. </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"> Thanks to @marypiper for suggesting this.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">-</span> Split ATAC-seq BAM files into nucleosome-free and mono/di/tri nucleosome files, so we can call </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"> peaks on them separately.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">-</span> Call peaks on NF/MN/DN/TN regions separately for each caller during ATAC-seq.</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">-</span> Allow viral contamination to be assasyed on non tumor/normal samples.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">-</span> Ensure EBV coverage is calculated when run on genomes with it included as a contig.</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 1.1.8 (28 October 2019)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="p">-</span> Add <span class="sb" style="color: #d14;">`antibody`</span> configuration option. Setting a specific antibody for ChIP-seq will use appropriate</span>
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3
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"> settings for that antibody. See the documentation for supported antibodies.</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="p">-</span> Add <span class="sb" style="color: #d14;">`use_lowfreq_filter`</span> for forcing vardict to report variants with low allelic frequency,</span>
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<li id="059a93c69080af2f6054c5324203b7af73cc5b83">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#059a93c69080af2f6054c5324203b7af73cc5b83"><strong>bcbio/bam/__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">@@ -403,11 +403,11 @@ def merge(bamfiles, out_bam, config):</td>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out_bam</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"coordinate"</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</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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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"coordinate"</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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407
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"> <span class="s" style="color: #d14;">"""Sort a BAM file, skipping if already present.</span></span>
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408
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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409
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">is_bam</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">),</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s in not a BAM file"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">in_bam</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bam_already_sorted</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="p">):</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">bam_already_sorted</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">in_bam</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">sort_stem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_sort_stem</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</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">@@ -579,3 +579,24 @@ def remove_duplicates(in_bam, data):</td>
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">out_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</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="LC581" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out_bam</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">count_alignments</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"><span class="s" style="color: #d14;"> count alignments in a BAM file passing a given filter. valid filter</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"><span class="s" style="color: #d14;"> strings are available in the sambamba documentation:</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"><span class="s" style="color: #d14;"> https://github.com/biod/sambamba/wiki/</span><span class="si" style="color: #d14;">%5</span><span class="s" style="color: #d14;">Bsambamba-view</span><span class="si" style="color: #d14;">%5</span><span class="s" style="color: #d14;">D-Filter-expression-syntax</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">sambamba</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"sambamba"</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</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="LC591" class="line" lang="python"> <span class="n" style="color: #333;">num_cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_num_cores</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="LC592" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">filter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">filter_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Counting alignments in {in_bam}."</span></span>
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<pre style="margin: 0;">+<span id="LC595" 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="LC596" class="line" lang="python"> <span class="n" style="color: #333;">filter_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--filter {filter}"</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Counting alignments in {in_bam} matching {filter}."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{sambamba} view -c --nthreads {num_cores} -f bam {filter_string} {in_bam}"</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span></pre>
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<li id="db6099147d782b81be3efa804f6a41b2a6b7ebf5">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#db6099147d782b81be3efa804f6a41b2a6b7ebf5"><strong>bcbio/broad/picardrun.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(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="98" style="width: 35px; color: rgba(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">@@ -98,9 +98,10 @@ def picard_reorder(picard, in_bam, ref_file, out_file):</td>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tx_tmpdir</span><span class="p">(</span><span class="n" style="color: #333;">picard</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">:</span></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">picard</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_config</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">dict_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.dict"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">ref_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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101
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">"INPUT"</span><span class="p">,</span> <span class="n" style="color: #333;">in_bam</span><span class="p">),</span></span>
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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"OUTPUT"</span><span class="p">,</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">),</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left">REFERENCE"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ref</span>_file</span><span class="p">),</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left">SEQUENCE_DICTIONARY"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dict</span>_file</span><span class="p">),</span></span>
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104
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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"ALLOW_INCOMPLETE_DICT_CONCORDANCE"</span><span class="p">,</span> <span class="s" style="color: #d14;">"true"</span><span class="p">),</span></span>
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105
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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"TMP_DIR"</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">)]</span></span>
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106
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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">picard</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"ReorderSam"</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#fb17eef4888c4f7198909ebc1616eb92a3fed380"><strong>bcbio/chipseq/__init__.py</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">toolz</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tz</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">@@ -10,17 +11,29 @@ from bcbio.ngsalign import bowtie2, bwa</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.distributed.transaction</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">file_transaction</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.provenance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">do</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.heterogeneity.chromhacks</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_mitochondrial_chroms</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.heterogeneity.chromhacks</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">get_mitochondrial_chroms</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">get_nonmitochondrial_chroms</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.chipseq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">atac</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clean_chipseq_alignment</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="LC19" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># lcr_bed = utils.get_in(data, ("genome_resources", "variation", "lcr"))</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_chip_method</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="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"atac"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shift_ATAC</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="LC23" class="line" lang="python"> <span class="n" style="color: #333;">work_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_bam</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="LC24" class="line" lang="python"> <span class="n" style="color: #333;">work_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</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="LC25" class="line" lang="python"> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</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="LC26" class="line" lang="python"> <span class="n" style="color: #333;">clean_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remove_nonassembled_chrom</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</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="LC27" class="line" lang="python"> <span class="n" style="color: #333;">clean_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remove_mitochondrial_reads</span><span class="p">(</span><span class="n" style="color: #333;">clean_bam</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="LC28" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atac</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">calculate_complexity_metrics</span><span class="p">(</span><span class="n" style="color: #333;">clean_bam</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="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_keep_multimapped</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="LC30" class="line" lang="python"> <span class="n" style="color: #333;">clean_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remove_multimappers</span><span class="p">(</span><span class="n" style="color: #333;">clean_bam</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_keep_duplicates</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="LC32" class="line" lang="python"> <span class="n" style="color: #333;">clean_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove_duplicates</span><span class="p">(</span><span class="n" style="color: #333;">clean_bam</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="LC33" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"work_bam"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clean_bam</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for ATAC-seq, brewak alignments into NF, mono/di/tri nucleosome BAM files</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"atac"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atac</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split_ATAC</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="LC37" class="line" lang="python"> <span class="n" style="color: #333;">encode_bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">([</span><span class="s" style="color: #d14;">"genome_resources"</span><span class="p">,</span> <span class="s" style="color: #d14;">"variation"</span><span class="p">,</span> <span class="s" style="color: #d14;">"encode_blacklist"</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="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">encode_bed</span><span class="p">:</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"work_bam"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remove_blacklist_regions</span><span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_bam</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">encode_bed</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'config'</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">@@ -35,6 +48,26 @@ def clean_chipseq_alignment(data):</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_bam</span><span class="p">(</span><span class="n" style="color: #333;">data</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="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="LC50" class="line" lang="python"></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;">remove_mitochondrial_reads</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</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="LC52" class="line" lang="python"> <span class="n" style="color: #333;">mito</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_mitochondrial_chroms</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="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">mito</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Mitochondrial chromosome not identified, skipping removal of "</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"mitochondrial reads from {bam_file}."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bam_file</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">nonmito</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_nonmitochondrial_chroms</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="LC58" class="line" lang="python"> <span class="n" style="color: #333;">mito_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</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;">"-noMito.bam"</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">mito_bam</span><span class="p">):</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mito_bam</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">samtools</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"samtools"</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">))</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">nonmito_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">nonmito</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">num_cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_num_cores</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">mito_bam</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_bam</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;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{samtools} view -bh -@ {num_cores} {bam_file} {nonmito_flag} "</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"> {tx_out_bam}"</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Removing mitochondrial reads on {','.join(mito)} from {bam_file}."</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</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;">return</span> <span class="n" style="color: #333;">mito_bam</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>
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38
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_multimappers</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">aligner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_aligner</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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40
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">aligner</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">@@ -50,13 +83,13 @@ def remove_multimappers(bam_file, data):</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">unique_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_file</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"When a BAM file is given as input, bcbio skips removal of "</span></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">"multimappers."</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;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"ChIP/ATAC-seq usually requires duplicate marking, but it was disabled."</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">unique_bam</span></span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_nonassembled_chrom</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</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="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">"""Remove non-assembled contigs from the BAM file"""</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</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="LC91" class="line" lang="python"> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</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="LC92" class="line" lang="python"> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">fai</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.fai"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">ref_file</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fai</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">inh</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,31 +176,35 @@ def _normalized_bam_coverage(name, bam_input, data):</td>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_compute_deeptools_matrix</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="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">extract_NF_regions</span></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="LC179" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">shift_ATAC</span></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="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"> extract the nucleosome free regions from the work_bam. These regions will</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> be < 100 bases</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"><span class="s" style="color: #d14;"> shift the ATAC-seq alignments</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">MAX_FRAG_LENGTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span></span>
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152
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">sieve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"alignmentSieve"</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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153
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">work_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_bam</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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154
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">num_cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_num_cores</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</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 class="idiff left right">NF</span>.bam"</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</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 class="idiff left right">NF</span>.log"</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right">NF</span>_bam"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_file</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</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 class="idiff left right">shifted</span>.bam"</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</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 class="idiff left right">shifted</span>.log"</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">utils</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right">work</span>_bam"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_file</span></span>
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159
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data</span></span>
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160
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">,</span> \</span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">log_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_log_file</span><span class="p">:</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">tx_unsorted_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx_out_file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".unsorted"</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{sieve} --bam ${work_bam} --outFile {tx_unsorted_bam} --ATACshift "</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--numberOfProcessors {num_cores} --maxFragmentLength {MAX_FRAG_LENGTH} "</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--minMappingQuality 10 "</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--filterMetrics {tx_log_file} "</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="s" style="color: #d14;">"Extract NF regions from {work_bam} to {tx_unsorted_bam}."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">tx_out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">tx_unsorted_bam</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"NF_bam"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_file</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">unsorted_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">out_file</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;">".unsorted.bam"</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">,</span> \</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">log_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_log_file</span><span class="p">:</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">tx_unsorted_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_file</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;">".tmp.bam"</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</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;">f</span><span class="s" style="color: #d14;">"{sieve} --verbose --bam {work_bam} --outFile {tx_unsorted_file} --ATACshift "</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--numberOfProcessors {num_cores} --maxFragmentLength 0 "</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--minFragmentLength 0 "</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--minMappingQuality 10 "</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--filterMetrics {tx_log_file} "</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Shifting ATAC-seq alignments in {work_bam} to {tx_unsorted_file}."</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># shifting can cause the file to become unsorted</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">sorted_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">tx_unsorted_file</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">force</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">sorted_file</span><span class="p">,</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">))</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"work_bam"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_file</span></span>
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173
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data</span></span></pre>
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<li id="e058999dc6b36492007fce47afb7a70ca8b25e3d">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#e058999dc6b36492007fce47afb7a70ca8b25e3d"><strong>bcbio/chipseq/atac.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">toolz</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tz</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">namedtuple</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">utils</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datadict</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dd</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">config_utils</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.distributed.transaction</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">file_transaction</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.provenance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">do</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bam</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ranges taken from Buenrostro, Nat. Methods 10, 1213–1218 (2013).</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">ATACRange</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'ATACRange'</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'label'</span><span class="p">,</span> <span class="s" style="color: #d14;">'min'</span><span class="p">,</span> <span class="s" style="color: #d14;">'max'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">ATACRanges</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"NF"</span><span class="p">:</span> <span class="n" style="color: #333;">ATACRange</span><span class="p">(</span><span class="s" style="color: #d14;">"NF"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">),</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">"MN"</span><span class="p">:</span> <span class="n" style="color: #333;">ATACRange</span><span class="p">(</span><span class="s" style="color: #d14;">"MN"</span><span class="p">,</span> <span class="mi" style="color: #099;">180</span><span class="p">,</span> <span class="mi" style="color: #099;">247</span><span class="p">),</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"DN"</span><span class="p">:</span> <span class="n" style="color: #333;">ATACRange</span><span class="p">(</span><span class="s" style="color: #d14;">"DN"</span><span class="p">,</span> <span class="mi" style="color: #099;">315</span><span class="p">,</span> <span class="mi" style="color: #099;">473</span><span class="p">),</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"TN"</span><span class="p">:</span> <span class="n" style="color: #333;">ATACRange</span><span class="p">(</span><span class="s" style="color: #d14;">"TN"</span><span class="p">,</span> <span class="mi" style="color: #099;">558</span><span class="p">,</span> <span class="mi" style="color: #099;">615</span><span class="p">)}</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calculate_complexity_metrics</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</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="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> the work_bam should have duplicates marked but not removed</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> mitochondrial reads should be removed </span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">bedtools</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"bedtools"</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</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="LC26" class="line" lang="python"> <span class="n" style="color: #333;">work_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_dir</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="LC27" class="line" lang="python"> <span class="n" style="color: #333;">metrics_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">work_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"metrics"</span><span class="p">,</span> <span class="s" style="color: #d14;">"atac"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">metrics_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">metrics_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">metrics_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{dd.get_sample_name(data)}-atac-metrics.csv"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">metrics_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assoc_in</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'atac'</span><span class="p">,</span> <span class="s" style="color: #d14;">'complexity_metrics_file'</span><span class="p">],</span> <span class="n" style="color: #333;">metrics_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># BAM file must be sorted by read name</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">work_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_config</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"queryname"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">metrics_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_metrics_file</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;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tx_metrics_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out_handle</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;">out_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"mt,m0,m1,m2</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="LC39" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{bedtools} bamtobed -bedpe -i {work_bam} | "</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"awk 'BEGIN{OFS=</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">}{print $1,$2,$4,$6,$9,$10}' | "</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"sort | "</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"uniq -c | "</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"awk 'BEGIN{mt=0;m0=0;m1=0;m2=0}($1==1){m1=m1+1} "</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"($1==2){m2=m2+1}{m0=m0+1}{mt=mt+$1}END{printf </span><span class="se" style="color: #d14;">\"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d,</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d,</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d,</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">n</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, mt,m0,m1,m2}' >> "</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{tx_metrics_file}"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Calculating ATAC-seq complexity metrics on {work_bam}, saving as {metrics_file}."</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assoc_in</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'atac'</span><span class="p">,</span> <span class="s" style="color: #d14;">'complexity_metrics_file'</span><span class="p">],</span> <span class="n" style="color: #333;">metrics_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" 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="LC50" class="line" lang="python"></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;">calculate_encode_complexity_metrics</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="LC52" class="line" lang="python"> <span class="n" style="color: #333;">metrics_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">([</span><span class="s" style="color: #d14;">'atac'</span><span class="p">,</span> <span class="s" style="color: #d14;">'complexity_metrics_file'</span><span class="p">],</span> <span class="n" style="color: #333;">data</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="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">metrics_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC55" 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="LC56" 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;">metrics_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">in_handle</span><span class="p">:</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">raw_metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">h</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">)}</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"PBC1"</span><span class="p">:</span> <span class="n" style="color: #333;">raw_metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"m1"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">raw_metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"m0"</span><span class="p">],</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">"NRF"</span><span class="p">:</span> <span class="n" style="color: #333;">raw_metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"m0"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">raw_metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"mt"</span><span class="p">]}</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">raw_metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"m2"</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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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">PBC2</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="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">PBC2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"m1"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">raw_metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"m2"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">metrics</span><span class="p">[</span><span class="s" style="color: #d14;">"PBC2"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PBC2</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">metrics</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">split_ATAC</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">bam_file</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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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;"> splits a BAM into nucleosome-free (NF) and mono/di/tri nucleosome BAMs based</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> on the estimated insert sizes</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> uses the current working BAM file if no BAM file is supplied</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">sambamba</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"sambamba"</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="LC76" class="line" lang="python"> <span class="n" style="color: #333;">num_cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_num_cores</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="LC77" class="line" lang="python"> <span class="n" style="color: #333;">base_cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'{sambamba} view --format bam --nthreads {num_cores} '</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">bam_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_file</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bam_file</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_bam</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="LC79" class="line" lang="python"> <span class="n" style="color: #333;">out_stem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">split_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">arange</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ATACRanges</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{out_stem}-{arange.label}.bam"</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</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;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base_cmd</span> <span class="o" style="font-weight: 600;">+</span>\</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'-F "template_length > {arange.min} and template_length < {arange.max}" '</span> <span class="o" style="font-weight: 600;">+</span>\</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'{bam_file} > {tx_out_file}'</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">'Splitting {arange.label} regions from {bam_file}.'</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">split_files</span><span class="p">[</span><span class="n" style="color: #333;">arange</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_file</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assoc_in</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'atac'</span><span class="p">,</span> <span class="s" style="color: #d14;">'align'</span><span class="p">],</span> <span class="n" style="color: #333;">split_files</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data</span></span></pre>
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<li id="4eabad8cbe351e3e3d7466ee25d9d970b164368a">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#4eabad8cbe351e3e3d7466ee25d9d970b164368a"><strong>bcbio/chipseq/macs2.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">@@ -9,6 +9,7 @@ from bcbio.pipeline import datadict as dd</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bam</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.chipseq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">antibodies</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.distributed.transaction</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">file_transaction</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">chip_bam</span><span class="p">,</span> <span class="n" style="color: #333;">input_bam</span><span class="p">,</span> <span class="n" style="color: #333;">genome_build</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="n" style="color: #333;">resources</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="LC15" 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">@@ -20,7 +21,7 @@ def run(name, chip_bam, input_bam, genome_build, out_dir, method, resources, dat</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_peaks_macs2.xls"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">macs2_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_peaks.xls"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">_compress_<span class="idiff left">bdg_files</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">out_dir</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">_compress_<span class="idiff left">and_sort_bdg_files</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">out_dir</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">data</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_get_output_files</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">macs2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"macs2"</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">antibody</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antibodies</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ANTIBODIES</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_antibody</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">(),</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(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">@@ -40,13 +41,13 @@ def run(name, chip_bam, input_bam, genome_build, out_dir, method, resources, dat</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="s" style="color: #d14;">"macs2 for </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">move_safe</span><span class="p">(</span><span class="n" style="color: #333;">macs2_file</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CalledProcessError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"macs2 terminated with an error.</span><span class="se" style="color: #d14;"><span class="idiff left right">\n</span></span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"macs2 terminated with an error.<span class="idiff left right"> </span>"</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"Please, check the message and report "</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"error if it is related to bcbio.</span><span class="se" style="color: #d14;"><span class="idiff left right">\n</span></span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"error if it is related to bcbio.<span class="idiff left right"> </span>"</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"You can add specific options for the sample "</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"setting resources as explained in docs: "</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#sample-specific-resources"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">_compress_<span class="idiff left">bdg_files</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">out_dir</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">_compress_<span class="idiff left">and_sort_bdg_files</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">out_dir</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">data</span></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;">return</span> <span class="n" style="color: #333;">_get_output_files</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_output_files</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</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">@@ -61,10 +62,16 @@ def _get_output_files(out_dir):</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="s" style="color: #d14;">"main"</span><span class="p">:</span> <span class="n" style="color: #333;">peaks</span><span class="p">,</span> <span class="s" style="color: #d14;">"macs2"</span><span class="p">:</span> <span class="n" style="color: #333;">fns</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_compress_<span class="idiff left">bdg_files</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">out_dir</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_compress_<span class="idiff left">and_sort_bdg_files</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">out_dir</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">data</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">glob</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"*bdg"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"gzip </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fn</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="s" style="color: #d14;">"compress bdg file: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fn</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".gz"</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">out_file</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;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">bedtools</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_program</span><span class="p">(</span><span class="s" style="color: #d14;">"bedtools"</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="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"{bedtools} sort -i {fn} | bgzip -c > {tx_out_file}"</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Compressing and sorting {fn}."</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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68
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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69
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_macs2_cmd</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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70
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"""Main command for macs2 tool."""</span></span>
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<li id="fbfb96675c481efdacfedf0214b473e7d623d79c">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#fbfb96675c481efdacfedf0214b473e7d623d79c"><strong>bcbio/chipseq/peaks.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">@@ -12,7 +12,7 @@ from bcbio.pipeline import config_utils</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datadict</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dd</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.provenance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">do</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.distributed.transaction</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">file_transaction</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.chipseq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">atac</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_callers</span><span class="p">():</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get functions related to each caller"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,18 +44,28 @@ def peakcall_prepare(data, run_parallel):</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calling</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="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"""Main function to parallelize peak calling."""</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">chip_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"work_bam"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">input_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"work_bam_input"</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="LC47" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_chip_method</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="LC48" class="line" lang="python"> <span class="n" style="color: #333;">caller_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_callers</span><span class="p">()[</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"peak_fn"</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</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="LC51" class="line" lang="python"> <span class="n" style="color: #333;">out_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"peak_fn"</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="LC52" class="line" lang="python"> <span class="n" style="color: #333;">out_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">caller_fn</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">chip_bam</span><span class="p">,</span> <span class="n" style="color: #333;">input_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_genome_build</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">out_dir</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;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_chip_method</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"resources"</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="LC54" class="line" lang="python"> <span class="n" style="color: #333;">greylistdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">greylisting</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="LC55" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="s" style="color: #d14;">"peaks_files"</span><span class="p">:</span> <span class="n" style="color: #333;">out_files</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># data["input_bam_filter"] = input_bam</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">greylistdir</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"greylist"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">greylistdir</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"chip"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">chip_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"work_bam"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">input_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"work_bam_input"</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="LC52" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</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="LC53" class="line" lang="python"> <span class="n" style="color: #333;">out_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"peak_fn"</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="LC54" class="line" lang="python"> <span class="n" style="color: #333;">out_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">caller_fn</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">chip_bam</span><span class="p">,</span> <span class="n" style="color: #333;">input_bam</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_genome_build</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">out_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_chip_method</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"resources"</span><span class="p">],</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">greylistdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">greylisting</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="s" style="color: #d14;">"peaks_files"</span><span class="p">:</span> <span class="n" style="color: #333;">out_files</span><span class="p">})</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">greylistdir</span><span class="p">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"greylist"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">greylistdir</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"atac"</span><span class="p">:</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fraction</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">atac</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ATACRanges</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">chip_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">((</span><span class="s" style="color: #d14;">"atac"</span><span class="p">,</span> <span class="s" style="color: #d14;">"align"</span><span class="p">,</span> <span class="n" style="color: #333;">fraction</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"Running peak calling with {data['peak_fn']} on the {fraction} fraction of {chip_bam}."</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"-{fraction}"</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">out_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"peak_fn"</span><span class="p">],</span> <span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">out_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">caller_fn</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">chip_bam</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_genome_build</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">out_dir</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_chip_method</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"resources"</span><span class="p">],</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assoc_in</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">"peaks_files"</span><span class="p">,</span> <span class="n" style="color: #333;">fraction</span><span class="p">),</span> <span class="n" style="color: #333;">out_files</span><span class="p">)</span></span>
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59
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_sync</span><span class="p">(</span><span class="n" style="color: #333;">original</span><span class="p">,</span> <span class="n" style="color: #333;">processed</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#fee19f4f498a2b34eca43fa79376fa526f252577"><strong>bcbio/heterogeneity/chromhacks.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">@@ -58,3 +58,16 @@ def get_mitochondrial_chroms(data):</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</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="LC59" class="line" lang="python"> <span class="n" style="color: #333;">mito</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</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;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_contigs</span><span class="p">(</span><span class="n" style="color: #333;">ref_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_mitochondrial</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mito</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_nonmitochondrial_chroms</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="LC63" class="line" lang="python"> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</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="LC64" class="line" lang="python"> <span class="n" style="color: #333;">nonmito</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</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;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_contigs</span><span class="p">(</span><span class="n" style="color: #333;">ref_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_mitochondrial</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nonmito</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_EBV</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="LC68" class="line" lang="python"> <span class="n" style="color: #333;">EBVCONTIGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"chrEBV"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EBV"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</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="LC70" 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;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_contigs</span><span class="p">(</span><span class="n" style="color: #333;">ref_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">EBVCONTIGS</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;">return</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</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">@@ -44,7 +44,7 @@ def align_bam(in_bam, ref_file, names, align_dir, data):</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">tx_out_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">prefix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-in1"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tx_out_prefix</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"unset JAVA_HOME && "</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"{samtools} sort -n -<span class="idiff left right">o -l 1 -@ {num_cores} -m {max_mem} {in_bam}</span> {prefix1} "</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"{samtools} sort -n -<span class="idiff left right">l 1 -@ {num_cores} -m {max_mem} {in_bam} -T</span> {prefix1} "</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"| {bedtools} bamtofastq -i /dev/stdin -fq /dev/stdout -fq2 /dev/stdout "</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"| {bwa_cmd} | "</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tobam_cl</span></span>
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<li id="bbb7842f2be9690f4ae67a1de2c07f322d6e261e">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#bbb7842f2be9690f4ae67a1de2c07f322d6e261e"><strong>bcbio/ngsalign/star.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">@@ -62,9 +62,10 @@ def align(fastq_file, pair_file, ref_file, names, align_dir, data):</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">ref_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">align_dir</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_align_dir</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;">tx_star_dirnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_star_dirnames</span><span class="p">(</span><span class="n" style="color: #333;">tx_align_dir</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">names</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;">tx_1pass_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx_align_dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"1pass"</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">tx_star_dirnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_star_dirnames</span><span class="p">(</span><span class="n" style="color: #333;">tx_1pass_dir</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">tx_out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">,</span> <span class="n" style="color: #333;">tx_out_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">tx_final_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx_star_dirnames</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">tx_<span class="idiff left right">align</span>_dir</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;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">tx_<span class="idiff left right">1pass</span>_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"{star_path} --genomeDir {ref_file} --readFilesIn {fastq_files} "</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">"--runThreadN {num_cores} --outFileNamePrefix {tx_out_prefix} "</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">@@ -104,7 +105,55 @@ def align(fastq_file, pair_file, ref_file, names, align_dir, data):</td>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">resources</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"options"</span><span class="p">,</span> <span class="p">[])])</span></span>
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105
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" | "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">postalign</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sam_to_sortbam_cl</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">tx_final_out</span><span class="p">)</span></span>
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106
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" > {tx_final_out} "</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">run_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Running STAR aligner on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s and </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_file</span><span class="p">,</span> <span class="n" style="color: #333;">ref_file</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">run_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Running 1st pass of STAR aligner on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s and </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_file</span><span class="p">,</span> <span class="n" style="color: #333;">ref_file</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="n" style="color: #333;">run_message</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">sjfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_splicejunction_file</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">sjflag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="s" style="color: #d14;">"--sjdbFileChrStartEnd {sjfile}"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sjfile</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">tx_star_dirnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_star_dirnames</span><span class="p">(</span><span class="n" style="color: #333;">tx_align_dir</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">tx_out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">,</span> <span class="n" style="color: #333;">tx_out_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">tx_final_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx_star_dirnames</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">tx_align_dir</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"{star_path} --genomeDir {ref_file} --readFilesIn {fastq_files} "</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">"--runThreadN {num_cores} --outFileNamePrefix {tx_out_prefix} "</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"--outReadsUnmapped Fastx --outFilterMultimapNmax {max_hits} "</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">"--outStd BAM_Unsorted {srna_opts} "</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">"--limitOutSJcollapsed 2000000 "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">"{sjflag} "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">"--outSAMtype BAM Unsorted "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">"--outSAMmapqUnique 60 "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"--outSAMunmapped Within --outSAMattributes </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s "</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">ALIGN_TAGS</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">_add_sj_index_commands</span><span class="p">(</span><span class="n" style="color: #333;">fastq_file</span><span class="p">,</span> <span class="n" style="color: #333;">ref_file</span><span class="p">,</span> <span class="n" style="color: #333;">gtf_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">srna</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">_read_group_option</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_fusion_caller</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"arriba"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_fusion_caller</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="s" style="color: #d14;">"--chimSegmentMin 10 --chimOutType WithinBAM SoftClip Junctions "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="s" style="color: #d14;">"--chimJunctionOverhangMin 10 --chimScoreMin 1 --chimScoreDropMax 30 "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="s" style="color: #d14;">"--chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">"--alignSJstitchMismatchNmax 5 -1 5 5 "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="s" style="color: #d14;">"--chimSegmentReadGapMax 3 "</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">" --chimSegmentMin 12 --chimJunctionOverhangMin 12 "</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="s" style="color: #d14;">"--chimScoreDropMax 30 --chimSegmentReadGapMax 5 "</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">"--chimScoreSeparation 5 "</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"oncofuse"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_fusion_caller</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"--chimOutType Junctions "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"--chimOutType WithinBAM "</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">"config"</span><span class="p">,</span> <span class="s" style="color: #d14;">"algorithm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"strandedness"</span><span class="p">),</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"unstranded"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"unstranded"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">srna</span><span class="p">:</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" --outSAMstrandField intronMotif "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">srna</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" --quantMode TranscriptomeSAM "</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_resources</span><span class="p">(</span><span class="s" style="color: #d14;">"star"</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"config"</span><span class="p">])</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resources</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"options"</span><span class="p">,</span> <span class="p">[]):</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">resources</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"options"</span><span class="p">,</span> <span class="p">[])])</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" | "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">postalign</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sam_to_sortbam_cl</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">tx_final_out</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" > {tx_final_out} "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">run_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Running 2nd pass of STAR aligner on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s and </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fastq_file</span><span class="p">,</span> <span class="n" style="color: #333;">ref_file</span><span class="p">)</span></span>
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108
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="n" style="color: #333;">run_message</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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109
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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110
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_update_data</span><span class="p">(</span><span class="n" style="color: #333;">star_dirs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">final_out</span><span class="p">,</span> <span class="n" style="color: #333;">star_dirs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#28669a7ddccdf8ac47c577727840379bba16c871"><strong>bcbio/pipeline/rnaseq.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">@@ -11,7 +11,8 @@ from bcbio.distributed.transaction import file_transaction</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fast_rnaseq</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_salmon_index"</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">samples</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">to_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">determine_indexes_to_make</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_salmon_index"</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">to_index</span><span class="p">])</span></span>
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15
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_salmon_reads"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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16
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_counts_spikein"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spikein</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">combine_spikein</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" style="width: 35px; color: rgba(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="206" style="width: 35px; color: rgba(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">@@ -205,6 +206,7 @@ def quantitate_expression_parallel(samples, run_parallel):</td>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;"> take advantage of the threaded run_parallel environment</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</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>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">to_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">determine_indexes_to_make</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"generate_transcript_counts"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"cufflinks"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_expression_caller</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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210
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_cufflinks"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(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="215" style="width: 35px; color: rgba(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">@@ -213,13 +215,14 @@ def quantitate_expression_parallel(samples, run_parallel):</td>
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213
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="s" style="color: #d14;">"kallisto"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_expression_caller</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span></span>
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214
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_fusion_mode</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span></span>
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215
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">"pizzly"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_fusion_caller</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">[])):</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">samples</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">run_parallel</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"run_kallisto_index"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">samples</span></span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">run_parallel</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"run_kallisto_index"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">to_index</span></span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_kallisto_rnaseq"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"sailfish"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_expression_caller</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">samples</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">run_parallel</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"run_sailfish_index"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">samples</span></span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">run_parallel</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"run_sailfish_index"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">to_index</span></span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_sailfish"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># always run salmon</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">run_parallel</span><span class="p">(</span><span class="s" style="color: #d14;">"run_salmon_index"</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">to_index</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_quantify_genome_alignments</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="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_aligner</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"star"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_genome_build</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"hg38"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="496" style="width: 35px; color: rgba(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">@@ -496,3 +499,25 @@ def combine_files(samples):</td>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_tx2gene</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">tx2gene_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">updated_samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">data</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">updated_samples</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">determine_indexes_to_make</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"><span class="s" style="color: #d14;"> returns a subset of the samples that have different indexes in them to make sure we only</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"><span class="s" style="color: #d14;"> make each index once</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">to_single_data</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="p">]</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">indexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">tomake</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">data</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="n" style="color: #333;">out_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_dir</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="s" style="color: #d14;">"inputs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"transcriptome"</span><span class="p">)</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">out_stem</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_genome_build</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">))</span></span>
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514
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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="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_disambiguate</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">out_stem</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">out_stem</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_disambiguate</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">[]))</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_disambiguate</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">out_stem</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">out_stem</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_disambiguate</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">[]))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">combined_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_stem</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fa"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">combined_file</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;">indexes</span><span class="p">:</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">tomake</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">indexes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">combined_file</span><span class="p">)</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tomake</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#6a5842dd9e3c5daac8e6d62a34e4d60ab86b78bf"><strong>bcbio/pipeline/run_info.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">@@ -11,6 +11,7 @@ import itertools</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">operator</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">string</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">toolz</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tz</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="331" style="width: 35px; color: rgba(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">@@ -331,6 +332,11 @@ def _clean_metadata(data):</td>
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331
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"metadata"</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;">data</span><span class="p">:</span></span>
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332
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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333
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">][</span><span class="s" style="color: #d14;">"batch"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-joint"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_analysis</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">((</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample"</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rna-seq"</span><span class="p">:</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"'sample' is a reserved keyword in metadata for RNA-seq. Please "</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="s" style="color: #d14;">"rename this column to something else and rerun."</span><span class="p">)</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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334
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<pre style="margin: 0;"> <span id="LC340" 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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335
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>
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336
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_clean_algorithm</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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<li id="fac91f905233560f253b7063f3b6889aeca3af62">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#fac91f905233560f253b7063f3b6889aeca3af62"><strong>bcbio/pipeline/sample.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(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">@@ -147,7 +147,8 @@ def process_alignment(data, alt_input=None):</td>
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147
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sort_method</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sort_method</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"coordinate"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot specify `bam_clean: picard` with `bam_sort` other than coordinate: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sort_method</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">out_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cleanbam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">picard_prep</span><span class="p">(</span><span class="n" style="color: #333;">fastq1</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"rgnames"</span><span class="p">],</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"dirs"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</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="LC151" class="line" lang="python"> <span class="n" style="color: #333;">out_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cleanbam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">picard_prep</span><span class="p">(</span><span class="n" style="color: #333;">fastq1</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"rgnames"</span><span class="p">],</span> <span class="n" style="color: #333;">ref_file</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"dirs"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC152" 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="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">bamclean</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fixrg"</span><span class="p">:</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">out_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cleanbam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixrg</span><span class="p">(</span><span class="n" style="color: #333;">fastq1</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"rgnames"</span><span class="p">],</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"dirs"</span><span class="p">],</span> <span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<li id="0b928052acb70b506a8457627983f038aaf8fd4d">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#0b928052acb70b506a8457627983f038aaf8fd4d"><strong>bcbio/qc/multiqc.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">@@ -34,6 +34,7 @@ from bcbio.variation import bedutils</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.qc.variant</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_active_vcinfo</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.upload</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_all_upload_paths_from_sample</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.variation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">coverage</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.chipseq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">atac</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">summary</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">samples</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"""Summarize all quality metrics together"""</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">@@ -447,6 +448,13 @@ def _add_disambiguate(sample):</td>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">sample</span><span class="p">[</span><span class="s" style="color: #d14;">"summary"</span><span class="p">][</span><span class="s" style="color: #d14;">"metrics"</span><span class="p">][</span><span class="s" style="color: #d14;">"Disambiguated ambiguous reads"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">disambigStats</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sample</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_atac</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">):</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">atac_metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atac</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">calculate_encode_complexity_metrics</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">)</span></span>
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453
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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="n" style="color: #333;">atac_metrics</span><span class="p">:</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sample</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">sample</span><span class="p">[</span><span class="s" style="color: #d14;">"summary"</span><span class="p">][</span><span class="s" style="color: #d14;">"metrics"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">atac_metrics</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">[</span><span class="s" style="color: #d14;">"summary"</span><span class="p">][</span><span class="s" style="color: #d14;">"metrics"</span><span class="p">])</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sample</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"></span>
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450
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_fix_duplicated_rate</span><span class="p">(</span><span class="n" style="color: #333;">dt</span><span class="p">):</span></span>
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451
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459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get RNA duplicated rate if exists and replace by samtools metric"""</span></span>
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452
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460
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Duplication_Rate_of_Mapped"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dt</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">@@ -461,6 +469,7 @@ def _merge_metrics(samples, out_dir):</td>
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461
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">sample_metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span></span>
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462
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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463
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471
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_add_disambiguate</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="LC472" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_add_atac</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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464
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">([</span><span class="s" style="color: #d14;">'summary'</span><span class="p">,</span> <span class="s" style="color: #d14;">'metrics'</span><span class="p">],</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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465
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">six</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">string_types</span><span class="p">):</span></span>
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466
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475
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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<li id="1632995720dec2c83890f793045a09678042e862">
<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#1632995720dec2c83890f793045a09678042e862"><strong>bcbio/qc/viral.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">@@ -11,6 +11,7 @@ from bcbio.distributed.transaction import file_transaction</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datadict</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dd</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.provenance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">do</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.variation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">vcfutils</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bcbio.heterogeneity</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chromhacks</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333;">bam_file</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run viral QC analysis:</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">@@ -21,39 +22,50 @@ def run(bam_file, data, out_dir):</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">source_link</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files'</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">viral_target</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"gdc-viral"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vcfutils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_paired_phenotype</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="LC25" class="line" lang="python"> <span class="n" style="color: #333;">viral_refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_viral_files</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.fa"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">viral_target</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">viral_refs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">viral_refs</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="LC27" class="line" lang="python"> <span class="n" style="color: #333;">viral_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">viral_refs</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="LC28" class="line" lang="python"> <span class="n" style="color: #333;">viral_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.bam"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</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="LC30" class="line" lang="python"> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">viral_ref</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="LC31" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-completeness.txt"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">viral_bam</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="LC32" class="line" lang="python"> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_num_cores</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="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_uptodate</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">bam_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_uptodate</span><span class="p">(</span><span class="n" style="color: #333;">viral_bam</span><span class="p">,</span> <span class="n" style="color: #333;">bam_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">viral_bam</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">tmpfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-tmp"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"samtools view -u -f 4 {bam_file} | "</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"bamtofastq collate=0 | "</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"bwa mem -t {cores} {viral_ref} - | "</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"bamsort tmpfile={tmpfile} inputthreads={cores} outputthreads={cores} "</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"inputformat=sam index=1 indexfilename={tx_out_file}.bai O={tx_out_file}"</span><span class="p">)</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="s" style="color: #d14;">"Align unmapped reads to viral genome"</span><span class="p">)</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">mosdepth_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">viral_bam</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"mosdepth -t {cores} {mosdepth_prefix} {viral_bam} -n --thresholds 1,5,25 --by "</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"<(awk 'BEGIN {{FS=</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">}}; {{print $1 FS </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> FS $2}}' {viral_ref}.fai) && "</span></span>
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<td class="diff-line-num old old_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"echo '## Viral sequences (from {source_link}) found in unmapped reads' > {tx_out_file} &&"</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"echo '## Sample: {sample_name}' >> {tx_out_file} && "</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"echo '#virus</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">size</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">depth</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1x</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">5x</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">25x' >> {tx_out_file} && "</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"paste <(zcat {mosdepth_prefix}.regions.bed.gz) <(zgrep -v ^# {mosdepth_prefix}.thresholds.bed.gz) | "</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"awk 'BEGIN {{FS=</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">}} {{ print $1 FS $3 FS $4 FS $10/$3 FS $11/$3 FS $12/$3}}' | "</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"sort -n -r -k 5,5 >> {tx_out_file}"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="s" style="color: #d14;">"Analyse coverage of viral genomes"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">"base"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_file</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">"secondary"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">viral_refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_viral_files</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.fa"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">viral_target</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">viral_refs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_exists</span><span class="p">(</span><span class="n" style="color: #333;">viral_refs</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="LC27" class="line" lang="python"> <span class="n" style="color: #333;">viral_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">viral_refs</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="LC28" class="line" lang="python"> <span class="n" style="color: #333;">viral_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">safe_makedir</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.bam"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</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="LC30" class="line" lang="python"> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">viral_ref</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="LC31" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-completeness.txt"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">viral_bam</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="LC32" class="line" lang="python"> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_num_cores</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_uptodate</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="n" style="color: #333;">bam_file</span><span class="p">):</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_uptodate</span><span class="p">(</span><span class="n" style="color: #333;">viral_bam</span><span class="p">,</span> <span class="n" style="color: #333;">bam_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">viral_bam</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">tmpfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-tmp"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">tx_out_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"samtools view -u -f 4 {bam_file} | "</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"bamtofastq collate=0 | "</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"bwa mem -t {cores} {viral_ref} - | "</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"bamsort tmpfile={tmpfile} inputthreads={cores} outputthreads={cores} "</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"inputformat=sam index=1 indexfilename={tx_out_file}.bai O={tx_out_file}"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="s" style="color: #d14;">"Align unmapped reads to viral genome"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">file_transaction</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tx_out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sample_name</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="LC45" class="line" lang="python"> <span class="n" style="color: #333;">mosdepth_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">viral_bam</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="LC46" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"mosdepth -t {cores} {mosdepth_prefix} {viral_bam} -n --thresholds 1,5,25 --by "</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"<(awk 'BEGIN {{FS=</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">}}; {{print $1 FS </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> FS $2}}' {viral_ref}.fai) && "</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"echo '## Viral sequences (from {source_link}) found in unmapped reads' > {tx_out_file} &&"</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"echo '## Sample: {sample_name}' >> {tx_out_file} && "</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"echo '#virus</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">size</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">depth</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1x</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">5x</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">25x' >> {tx_out_file} && "</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"paste <(zcat {mosdepth_prefix}.regions.bed.gz) <(zgrep -v ^# {mosdepth_prefix}.thresholds.bed.gz) | "</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"awk 'BEGIN {{FS=</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">}} {{ print $1 FS $3 FS $4 FS $10/$3 FS $11/$3 FS $12/$3}}' | "</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"sort -n -r -k 5,5 >> {tx_out_file}"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="s" style="color: #d14;">"Analyse coverage of viral genomes"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chromhacks</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_EBV</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="LC56" class="line" lang="python"> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_ref_file</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="LC57" class="line" lang="python"> <span class="n" style="color: #333;">work_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_work_bam</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="LC58" class="line" lang="python"> <span class="n" style="color: #333;">ebv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chromhacks</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_EBV</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="LC59" class="line" lang="python"> <span class="n" style="color: #333;">mosdepth_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">work_bam</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;">"-EBV"</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"mosdepth -t {cores} {mosdepth_prefix} {work_bam} -n --thresholds 1,5,25 --by "</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">"<(grep {ebv} {ref_file}.fai | awk 'BEGIN {{FS=</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">}}; {{print $1 FS </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> FS $2}}') && "</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"paste <(zcat {mosdepth_prefix}.regions.bed.gz) <(zgrep -v ^# {mosdepth_prefix}.thresholds.bed.gz) | "</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">"awk 'BEGIN {{FS=</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">}} {{ print $1 FS $3 FS $4 FS $10/$3 FS $11/$3 FS $12/$3}}' | "</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">"sort -n -r -k 5,5 >> {tx_out_file}"</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;">do</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="s" style="color: #d14;">"Analyse coverage of EBV"</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">"base"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_file</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">"secondary"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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57
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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59
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_files</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#953a5484c194dec73486a5e85ad272cd898cbf31"><strong>bcbio/upload/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(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">@@ -118,6 +118,7 @@ def _get_files_chipseq(sample):</td>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">algorithm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">[</span><span class="s" style="color: #d14;">"config"</span><span class="p">][</span><span class="s" style="color: #d14;">"algorithm"</span><span class="p">]</span></span>
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119
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_maybe_add_summary</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_maybe_add_alignment</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_maybe_add_nucleosome_alignments</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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121
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_maybe_add_peaks</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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122
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_maybe_add_greylist</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_add_meta</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">sample</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">@@ -493,6 +494,17 @@ def _maybe_add_transcriptome_alignment(sample, out):</td>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"> <span class="s" style="color: #d14;">"ext"</span><span class="p">:</span> <span class="s" style="color: #d14;">"transcriptome"</span><span class="p">})</span></span>
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_maybe_add_nucleosome_alignments</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"><span class="s" style="color: #d14;"> for ATAC-seq, also upload NF, MN, DN and TN bam files</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"> <span class="n" style="color: #333;">atac_align</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">((</span><span class="s" style="color: #d14;">"atac"</span><span class="p">,</span> <span class="s" style="color: #d14;">"align"</span><span class="p">),</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="p">{})</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">alignment</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">atac_align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">"path"</span><span class="p">:</span> <span class="n" style="color: #333;">atac_align</span><span class="p">[</span><span class="n" style="color: #333;">alignment</span><span class="p">],</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"> <span class="s" style="color: #d14;">"type"</span><span class="p">:</span> <span class="s" style="color: #d14;">"bam"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"> <span class="s" style="color: #d14;">"ext"</span><span class="p">:</span> <span class="n" style="color: #333;">alignment</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"></span>
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_maybe_add_counts</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">dd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_count_file</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</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">@@ -650,14 +662,25 @@ def _maybe_add_trna(algorithm, sample, out):</td>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_maybe_add_peaks</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"> <span class="n" style="color: #333;">out_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"peaks_files"</span><span class="p">,</span> <span class="p">{})</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">caller</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">out_dir</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">caller</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"main"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">out_dir</span><span class="p">[</span><span class="n" style="color: #333;">caller</span><span class="p">]:</span></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">"path"</span><span class="p">:</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="python"> <span class="s" style="color: #d14;">"dir"</span><span class="p">:</span> <span class="n" style="color: #333;">caller</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python"> <span class="s" style="color: #d14;">"ext"</span><span class="p">:</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">fn</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="LC665" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"NF"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">out_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">files</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">out_dir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">caller</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">caller</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"main"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">caller</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">"path"</span><span class="p">:</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="python"> <span class="s" style="color: #d14;">"dir"</span><span class="p">:</span> <span class="n" style="color: #333;">caller</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"> <span class="s" style="color: #d14;">"ext"</span><span class="p">:</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">fn</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="LC675" 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="LC676" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">caller</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">out_dir</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">caller</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"main"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">out_dir</span><span class="p">[</span><span class="n" style="color: #333;">caller</span><span class="p">]:</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">"path"</span><span class="p">:</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="s" style="color: #d14;">"dir"</span><span class="p">:</span> <span class="n" style="color: #333;">caller</span><span class="p">,</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"> <span class="s" style="color: #d14;">"ext"</span><span class="p">:</span> <span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext_plus</span><span class="p">(</span><span class="n" style="color: #333;">fn</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="LC684" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"></span>
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686
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_maybe_add_greylist</span><span class="p">(</span><span class="n" style="color: #333;">algorithm</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#b5f97c2465c41ae9654e19860697f479dc1cf205"><strong>bcbio/variation/effects.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(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">@@ -139,13 +139,13 @@ def get_vep_cache(dbkey, ref_file, tooldir=None, config=None):</td>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">safe_load</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">ensembl_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tz</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_in</span><span class="p">([</span><span class="s" style="color: #d14;">"aliases"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ensembl"</span><span class="p">],</span> <span class="n" style="color: #333;">resources</span><span class="p">)</span></span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">symlink_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_special_dbkey_maps</span><span class="p">(</span><span class="n" style="color: #333;">dbkey</span><span class="p">,</span> <span class="n" style="color: #333;">ref_file</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ensembl_name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ensembl_name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"_vep_"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" 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;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s has ensembl an incorrect value."</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="s" style="color: #d14;">"It should have _vep_ in the name."</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"Remove line or fix the name to avoid error."</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">symlink_dir</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ensembl_name</span><span class="p">:</span></span>
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147
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">species</span><span class="p">,</span> <span class="n" style="color: #333;">vepv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ensembl_name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_vep_"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">symlink_dir</span><span class="p">,</span> <span class="n" style="color: #333;">species</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">ensembl_name</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">species</span><span class="p">,</span> <span class="n" style="color: #333;">vepv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ensembl_name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_vep_"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">vep_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normpath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">ref_file</span><span class="p">)),</span> <span class="s" style="color: #d14;">"vep"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vep_dir</span><span class="p">,</span> <span class="n" style="color: #333;">species</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_vep</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#f1753c26ad7dd9c07a75161a266af4cb354610d3"><strong>docs/contents/configuration.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1050,9 +1050,7 @@ ChIP/ATAC sequencing</td>
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="plaintext">- ``aligner`` Currently ``bowtie2`` is the only one tested. ``bwa`` is also available.</span>
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="plaintext">- The ``phenotype`` and ``batch`` tags need to be set under ``metadata`` in the config YAML file. The ``phenotype`` tag will specify the chip (``phenotype: chip``) and input samples (``phenotype: input``). The ``batch`` tag will specify the input-chip pairs of samples for example, ``batch: pair1``. Same input can be used for different chip samples giving a list of distinct values: ``batch: [sample1, sample2]``.</span>
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="plaintext">- ``chip_method``: currently supporting standard CHIP-seq (TF or broad regions using `chip`) or ATAC-seq (`atac`). Parameters will change depending on the option to get the best possible results. Only macs2 supported for now.</span>
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<pre style="margin: 0;">-<span id="LC1053" class="line" lang="plaintext">- ``antibody``: automatically sets peakcalling options tailored for the specific anitbody. Supports</span>
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<pre style="margin: 0;">-<span id="LC1054" class="line" lang="plaintext">`h3f3a`, `h3k27me3`, `h3k36me3`, `h3k4me1`, `h3k79me2`, `h3k9me3`, `h3k9me1`, `h3k9me2`, `h4k20me1`,</span>
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<pre style="margin: 0;">-<span id="LC1055" class="line" lang="plaintext">`h2afz`, `h3ac`, `h3k27ac`, `h3k4me2`, `h3k4me3`, `h3k9ac`, `h3k9me3`.</span>
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="plaintext">- ``antibody``: automatically sets peakcalling options tailored for the specific anitbody. Supports `h3f3a`, `h3k27me3`, `h3k36me3`, `h3k4me1`, `h3k79me2`, `h3k9me3`, `h3k9me1`, `h3k9me2`, `h4k20me1`, `h2afz`, `h3ac`, `h3k27ac`, `h3k4me2`, `h3k4me3`, `h3k9ac`, `h3k9me3`.</span>
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="plaintext">- ``keep_duplicates``: do not remove duplicates before peak calling. Defaults to `False`.</span>
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="plaintext">- ``keep_multimapped``: do not remove multimappers before peak calling. Defaults to `False`.</span>
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1544,11 +1542,13 @@ Adding custom genomes</td>
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="plaintext">``bcbio_setup_genome.py`` will help you to install a custom genome and apply all changes needed</span>
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="plaintext">to the configuration files. It needs the genome in FASTA format, and the annotation file</span>
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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="plaintext">in GTF or GFF3 format. It can create index for all aligners used by bcbio. Moreover, it will create</span>
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<pre style="margin: 0;">-<span id="LC1547" class="line" lang="plaintext">the folder `rnaseq` to allow you run the RNAseq pipeline without further configuration.</span>
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="plaintext">the folder `rnaseq` to allow you run the RNAseq pipeline without further configuration. The ``--buildversion``</span>
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="plaintext">option will write that string to the ``version.txt`` file, to track from where and which version of</span>
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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="plaintext">a gene build was used.</span>
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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1549" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;"> <span id="LC1550" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC1551" class="line" lang="plaintext"> bcbio_setup_genome.py -f genome.fa -g annotation.gtf -i bowtie2 star seq -n Celegans -b WBcel135</span>
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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="plaintext"> bcbio_setup_genome.py -f genome.fa -g annotation.gtf -i bowtie2 star seq -n Celegans -b WBcel135<span class="idiff left right"> --buildversion WormBase_34</span></span>
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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="plaintext">If you want to add smallRNA-seq data files, you will need to add the 3 letters code of mirbase</span>
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<pre style="margin: 0;"> <span id="LC1554" class="line" lang="plaintext">for your genome (i.e hsa for human) and the GTF file for the annotation of smallRNA data.</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">@@ -1556,7 +1556,7 @@ Here you can use the same file than the transcriptome if no other available.</td>
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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;">-<span id="LC1559" class="line" lang="plaintext"> bcbio_setup_genome.py -f genome.fa -g annotation.gtf -i bowtie2 star seq -n Celegans -b WBcel135 --species cel --srna_gtf another_annotation.gtf</span>
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<pre style="margin: 0;">+<span id="LC1559" class="line" lang="plaintext"> bcbio_setup_genome.py -f genome.fa -g annotation.gtf -i bowtie2 star seq -n Celegans -b WBcel135 --species cel --srna_gtf another_annotation.gtf<span class="idiff left right"> --buildversion WormBase_34</span></span>
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<pre style="margin: 0;"> <span id="LC1560" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="plaintext">To use that genome just need to configure your YAML files as::</span>
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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#46caee1d50ca05a5fb7d450ccc1f3934ae0c9bc3"><strong>docs/contents/internals.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,7 +268,8 @@ bcbio.yaml config::</td>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"> --bc2 harvard-indrop-v3-cb2.txt.gz demultiplexed/[sample-barcodeAATTTTT].fq | \</span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext"> gzip -c > project-sample_barcode.filtered.fq.gz</span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext">- step 4*: create cellular barcode histrogram::</span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">- step 4*: create cellular barcode histogram, also creates cb-histogram-filtered.txt for cells</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> with nreads > minimum_barcode_depth::</span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext"> python umis cb_histogram project-sample_barcode.filtered.fq.gz > cb-histogram.txt</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">@@ -301,3 +302,13 @@ bcbio.yaml config::</td>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="plaintext">- step 8. Concatenate all cb-histogram-filtered.txt files::</span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext"> cat project-[all-barcodes]/cb-histogram-filtered.txt > cb-histogram.txt</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">Tests</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">~~~~~</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">To run bcbio automated tests, install bcbio and clone bcbio master repository. You are testing your installation with tests provided in bcbio-nextgen/tests::</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> which bcbio_nextgen.py</span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> cd bcbio-nextgen/tests</span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> ./run_tests.sh > tests.out</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">Tests are in integration/*.py. Each test has a set or marks. Marks are listed in pytest.ini. The mark defines how many tests to select. By default (just running plain ./run_tests.sh), it is speed1 = 11 tests. </span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#25f1fbed65859fbfcdb276507ddb9f56ebb11056"><strong>docs/contents/outputs.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,7 @@ Project directory</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">- ``multiqc`` run `MultiQC`_ to gather all QC metrics from different tools, such as,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> cutadapt, featureCounts, samtools, STAR ... into an unique HTML report.</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">- ``metadata.csv`` -- CSV with the metadata in the YAML file.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">- ``data_versions.csv`` -- Data versions for bcbio-nextgen and software</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">.. _MultiQC: http://multiqc.info</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,29 +69,70 @@ RNA-seq</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">Project directory</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">- ``annotated_combined.counts`` -- featureCounts counts matrix</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> with gene symbol as an extra column.</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">- ``combined.counts`` -- featureCounts counts matrix</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> with gene symbol as an extra column.</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">- ``combined.dexseq`` -- DEXseq counts matrix with</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> exonID as first column.</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">- ``combined.gene.sf.tmp`` -- Sailfish gene count</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> matrix normalized to TPM.</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">- ``combined.isoform.sf.tpm`` -- Sailfish transcript</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> count matix normalized to TPM.</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">- ``combined.sf`` -- Sailfish raw output, all samples</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> files are pasted one after another.</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">- ``tx2gene.csv`` -- Annotation file needed for DESeq2</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> to use Sailfish output.</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">| ├── annotated_combined.counts -- gene counts with symbols from featureCounts (don't use this)</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">| ├── bcbio-nextgen-commands.log -- commands run by bcbio</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">| ├── bcbio-nextgen.log -- logging information from bcbio run</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">| ├── combined.counts -- gene counts with gene IDs from featureCounts (don't use this)</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">| ├── metadata.csv -- provided metadata about each sample</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">| ├── multiqc</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">| ├── multiqc_report.html -- multiQC report</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">| ├── programs.txt -- program versions of tools run</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">| ├── project-summary.yaml -- YAML description of project, with derived metadata</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">| └── tx2gene.csv -- transcript to gene mappings for use with tximport</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">Sample directories</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">- ``SAMPLE-transcriptome.bam`` -- BAM file aligned to transcriptome.</span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">- ``SAMPLE-ready.counts`` -- featureCounts gene counts output.</span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">- ``salmon`` -- Salmon output.</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">single cell RNA-seq</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">| S1</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">| ├── S1-ready.bam -- coordinate-sorted whole genome alignments</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">| ├── S1-ready.counts -- featureCounts counts (don't use this)</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">| ├── S1-transcriptome.bam -- alignments to the transcriptome</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">| ├── salmon</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">| │ ├── abundance.h5 -- h5 object, usable with `sleuth`_</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">| │ └── quant.sf -- salmon quantifications, usable with `tximport`_</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">| └── STAR</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">| ├── S1-SJ.bed -- STAR junction file in BED format</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">| └── S1-SJ.tab -- STAR junction file in tabular format</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">bcbioRNASeq directory</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">| bcbioRNASeq/</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">| ├── data</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">| │ ├── bcb.rda -- `bcbioRNASeq`_ object with gene-level data</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">| ├── data-transcript</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">| │ ├── bcb.rda -- `bcbioRNASeq`_ object with transcript-level data</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">| ├── quality_control.html -- quality control report</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">| ├── quality_control.Rmd -- RMarkdown that generated quality control report</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">| ├── results</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">| │ └── 2019-11-21</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">| │ ├── gene -- gene level information</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">| │ │ └── counts</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">| │ │ ├── counts.csv.gz -- count matrix from tximport, suitable for count-based analyses</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">| │ │ └── metadata.csv.gz -- metadata and quality control data for samples</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">| │ ├── quality_control</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">| │ │ └── tpm.csv.gz -- TPM from tximport, use for visualization</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">| │ └── transcript -- transcript level information</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">| │ └── counts</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">| │ ├── counts.csv.gz -- transcript level count matrix, suitable for count-based analyses needed transcript-level data</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">| │ └── metadata.csv.gz -- metadata and quality control for samples</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">.. _sleuth: http://seqcluster.readthedocs.io/mirna_annotation.html</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">.. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.. _bcbioRNASeq: https://bioinformatics.sph.harvard.edu/bcbioRNASeq/</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">Workflow for analysis</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">For gene-level analyses, we recommend loading the gene-level counts.csv.gz and the metadata.csv.gz and using `DESeq2`_ to do the analysis. For a more in-depth walkthrough of how to use DESeq2, refer to our `DGE_workshop`_.</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">For transcript-level analyses, we recommend using `sleuth`_ with the bootstrap samples. You can load the abundance.h5 files from Salmon, or if you set ``kallisto`` as an expression caller, use the abundance.h5 files from that.</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">Another great alternative is to use the Salmon quantification to look at differential transcript usage (DTU) instead of differential transcript expression (DTE). The idea behind DTU is you are looking for transcripts of genes that have been flipped from one isoform to another. The `Swimming downstream`_ tutorial has a nice walkthrough of how to do that.</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.. _DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.. _DGE_workshop: https://hbctraining.github.io/DGE_workshop_salmon/schedule/</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.. _Swimming downstream: http://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html#salmon-quantification</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">single cell RNA-Seq</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">===================</span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">Project directory</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">@@ -174,6 +216,32 @@ Sample directories</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="plaintext">.. _seqcluster: https://github.com/lpantano/seqcluster</span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">.. _tdrmapper: https://github.com/sararselitsky/tDRmapper</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">ATAC-seq</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">========</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">Sample directories</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">Below is an example sample directory for a sample called `rep1`. There are four</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">sets of peak files for each sample, for each peak caller, one set for each of</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">the nucleosome-free (NF), mononucleosome (MF), dinucleosome (DF) and trinucleosome</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">(TF) regions. There are BAM files of reach of those regions as well.</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">| rep1</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">| ├── macs2 -- peak calls from macs2</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">| │ ├── rep1-NF_control_lambda.bdg.gz -- local lambda estimate for poisson distribution from control samples in bedgraph format, NF regions only</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">| │ ├── rep1-NF_peaks.narrowpeak -- peaks in `narrowPeak`_ format in NF regions</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">| │ ├── rep1-NF_summits.bed -- top of peak in bed format of NF regions</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">| │ └── rep1-NF_treat_pileup.bdg.gz -- bedgraph for rep1 sample of NF regions</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">| ├── rep1-NF.bam -- BAM of just nucleosome free regions</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">| ├── rep1-MN.bam -- BAM of just mononucleosome regions</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">| ├── rep1-DN.bam -- BAM of just dinucleosome regions</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">| ├── rep1-TN.bam -- BAM of just trinucleosome regions</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">| ├── rep1-ready.bam -- BAM of all alignments</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">| └── rep1-ready.bw -- bigwig file of all alignments</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">.. _narrowPeak: http://genome.ucsc.edu/faq/faqformat.html#format12</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext">Downstream analysis</span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext">===================</span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#b1655f936472b3a6a6a310218f78e1d19987454b"><strong>requirements-conda.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bcbio-nextgen=1.1.<span class="idiff left right">7</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcbio-nextgen=1.1.<span class="idiff left right">8</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/bcbio-nextgen" rel="nofollow noreferrer noopener" target="_blank">bcbio-nextgen</a>==1.1.<span class="idiff left right">7</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/bcbio-nextgen" rel="nofollow noreferrer noopener" target="_blank">bcbio-nextgen</a>==1.1.<span class="idiff left right">8</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#bacc76312ae1e30f71298a0e5abf86c8e5dbec70"><strong>scripts/bcbio_setup_genome.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">@@ -237,7 +237,9 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Add ERCC spike-ins."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--mirbase"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"species in mirbase for smallRNAseq data."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--srna_gtf"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gtf to use for smallRNAseq data."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--buildversion"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"String describing build of genome used. Examples: "</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">"Ensembl_94, EnsemblMetazoa_94, Flybase_21, etc"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not all([args.mirbase, args.srna_gtf]) and any([args.mirbase, args.srna_gtf]):</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># raise ValueError("--mirbase and --srna_gtf both need a value.")</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">@@ -306,7 +308,7 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gtf</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="s" style="color: #d14;">"Preparing transcriptome."</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">build_dir</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pardir</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"{sys.executable} {prepare_tx} --cores {args.cores} --genome-dir {genome_dir} "</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"{sys.executable} {prepare_tx} --<span class="idiff left right">buildversion {args.buildversion} --</span>cores {args.cores} --genome-dir {genome_dir} "</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="s" style="color: #d14;">"--gtf {gtf_file} {args.name} {args.build}"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="nb" style="color: #0086b3;">locals</span><span class="p">()),</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mirbase</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">find_packages</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC7" 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;">"1.1.<span class="idiff left right">8</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC7" 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;">"1.1.<span class="idiff left right">9a</span>"</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_version_py</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">version_py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">'bcbio'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pipeline'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#c493fa11b32390866834a9938a57d281ac430b70"><strong>tests/data/atac/atac_1.fq</strong></a>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#4996eb58871bb817700228bd24171ab56ceaa95c"><strong>tests/data/atac/atac_2.fq</strong></a>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#ca1b3dbd209bf79f801b5a187faa2998b349c033"><strong>tests/data/automated/run_info-atacseq.yaml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">upload</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"> <span class="na" style="color: #008080;">dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">upload</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">details</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="na" style="color: #008080;">analysis</span><span class="pi">:</span> <span class="s" style="color: #d14;">chip-seq</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">files</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">../data/atac/atac_1.fq</span><span class="pi">,</span> <span class="nv" style="color: #008080;">../data/atac/atac_2.fq</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">algorithm</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">chip_method</span><span class="pi">:</span> <span class="s" style="color: #d14;">atac</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">aligner</span><span class="pi">:</span> <span class="s" style="color: #d14;">bwa</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">adapters</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">truseq</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">peakcaller</span><span class="pi">:</span> <span class="s" style="color: #d14;">macs2</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">keep_multimapped</span><span class="pi">:</span> <span class="s" style="color: #d14;">False</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">keep_duplicates</span><span class="pi">:</span> <span class="s" style="color: #d14;">False</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test1</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">genome_build</span><span class="pi">:</span> <span class="s" style="color: #d14;">mm9</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">metadata</span><span class="pi">:</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">batch</span><span class="pi">:</span> <span class="s" style="color: #d14;">b1</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">phenotype</span><span class="pi">:</span> <span class="s" style="color: #d14;">input</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#b2ff7250c9f6e5d3abe1718225f05b9c670270b2"><strong>tests/data/automated/run_info-chipseq.yaml</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">@@ -2,7 +2,7 @@ upload:</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"> <span class="na" style="color: #008080;">dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">upload</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">details</span><span class="pi">:</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">analysis</span><span class="pi">:</span> <span class="s" style="color: #d14;">chip-seq</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">files</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;"><span class="idiff left">'</span></span><span class="s" style="color: #d14;"><span class="idiff right">../data/test_chipseq/Hsapiens_Mmusculus_1.fq'</span></span><span class="pi">]</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">files</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;"><span class="idiff left right">../data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_1_fastq.txt</span></span><span class="pi">]</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">algorithm</span><span class="pi">:</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">aligner</span><span class="pi">:</span> <span class="s" style="color: #d14;">bwa</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">quality_format</span><span class="pi">:</span> <span class="s" style="color: #d14;">Standard</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#2e946528151ae7bd001de04d59a142da8ee2df0c"><strong>tests/integration/test_automated_analysis.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(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="189" style="width: 35px; color: rgba(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">@@ -189,6 +189,17 @@ def test_chipseq(install_test_files, data_dir):</td>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"run_info-chipseq.yaml"</span><span class="p">)]</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">cl</span><span class="p">)</span></span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atacseq</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_atacseq</span><span class="p">(</span><span class="n" style="color: #333;">install_test_files</span><span class="p">,</span> <span class="n" style="color: #333;">data_dir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> Test ATAC-seq pipeline</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">workdir</span><span class="p">:</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">cl</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"bcbio_nextgen.py"</span><span class="p">,</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">get_post_process_yaml</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="n" style="color: #333;">workdir</span><span class="p">),</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pardir</span><span class="p">,</span> <span class="s" style="color: #d14;">"test_atacseq"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"run_info-atacseq.yaml"</span><span class="p">)]</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">cl</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">speed1</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ensemble</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f#638319436d10230518a06abc53d6225665c74c4e"><strong>tests/pytest.ini</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">@@ -50,3 +50,4 @@ markers =</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">explant:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">test</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">explant</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">disambiguation</span></span>
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51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">chipseq:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">test</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ChIP-seq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pipeline</span></span>
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52
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ericscript:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">test</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Ericscript</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">integration</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">atacseq:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">test</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ATAC-seq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pipeline</span></span></pre>
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