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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/rosa">Debian Med / rosa</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rosa/-/commit/a3aa3f6815adfcab85bee65c14f4b29dcfc3d9a5">a3aa3f68</a></strong>
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<span>by Steffen Möller</span>
<i>at 2020-07-04T12:32:10+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added rosa package, fixed lintian warning
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</li>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/rosa/-/commit/a3aa3f6815adfcab85bee65c14f4b29dcfc3d9a5#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(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">@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> r-cran-lsd</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># sambamba <!nocheck></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/bartongroup/RoSA</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/rosa</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(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">@@ -16,6 +17,41 @@ Vcs-Git: https://salsa.debian.org/med-team/rosa.git</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Package: rosa</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Depends: r-other-rosa,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python3-rosa,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Description: Removal of Spurious Antisense in biological RNA sequences</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> In stranded RNA-Seq experiments it is possible to detect and</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> measure antisense transcription, important since antisense transcripts</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> impact gene transcription in several different ways. Stranded RNA-Seq</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> determines the strand from which an RNA fragment originates, and so can</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> be used to identify where antisense transcription may be implicated in</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> gene regulation.</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"> However, spurious antisense reads are often present in experiments, and</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> can manifest at levels greater than 1% of sense transcript levels. This</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> is enough to disrupt analyses by causing false antisense counts to</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> dominate the set of genes with high antisense transcription levels.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> The RoSA (Removal of Spurious Antisense) tool detects the presence of</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> high levels of spurious antisense transcripts, by:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> * analysing ERCC spike-in data to find the ratio of antisense:sense</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> transcripts in the spike-ins; or</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> * using antisense and sense counts around splice sites to provide a</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> set of gene-specific estimates; or</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> * both.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> Once RoSA has an estimate of the spurious antisense, expressed as a</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> ratio of antisense:sense counts, RoSA will calculate a correction to</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> the antisense counts based on the ratio. Where a gene-specific estimate</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> is available for a gene, it will be used in preference to the global</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> estimate obtained from either spike-ins or spliced reads.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> This package provides the library for the statistics suite R.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">Package: r-other-rosa</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">Section: gnu-r</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">@@ -55,8 +91,9 @@ Package: python3-rosa</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">Recommends: rosa</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">Recommends: r-other-rosa,</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> sambamba</span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">Description: Removal of Spurious Antisense in biological RNA sequences (Python3)</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"> In stranded RNA-Seq experiments it is possible to detect and</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> measure antisense transcription, important since antisense transcripts</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/rosa/-/commit/a3aa3f6815adfcab85bee65c14f4b29dcfc3d9a5#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,12 +18,12 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh_auto_install -O--buildsystem=R --sourcedirectory=$(CURDIR)</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> mv debian/tmp tmp-install</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> dh_auto_install --sourcedirectory=python --buildsystem=pybuild</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <span class="idiff left right">#cd python && ( [ -r debian ] || ln -s ../debian . ) && pybuild --install</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> <span class="idiff left right">find debian/python3-rosa -name *.csv | xargs -r chmod -x</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> rm -rf debian/rosa debian/tmp/ debian/python3-rosa</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> rm -rf python/.pybuild rm -rf python/rosa.egg-info</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> rm -rf python/.pybuild rm -rf python/rosa.egg-info<span class="idiff left right"> python/rosa/__pycache__ python/rosa/tests/__pycache__ python/.pytest_cache .pybuild tmp-install</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> rm -f python/debian</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"># FIXME: override_dh_auto_test:</span></pre>
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