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<h3>
Étienne Mollier pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kineticstools">Debian Med / kineticstools</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/kineticstools/-/commit/cde481528bb724dd09e404cdcb7cdbc33b203226">cde48152</a></strong>
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<span>by Etienne Mollier</span>
<i>at 2020-11-25T22:02:53+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.1+git20200729.e3723e0+dfsg</pre>
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<h4>2 changed files:</h4>
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<a href="#b12f5ac0052d9237edaacf8bc73366288bda6ce3">
kineticsTools/MultiSiteCommon.py
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<a href="#3de438878d25828a21fc72e3e303cd3d341e4def">
test/test_integration.py
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<h4>Changes:</h4>
<li id="b12f5ac0052d9237edaacf8bc73366288bda6ce3">
<a href="https://salsa.debian.org/med-team/kineticstools/-/commit/cde481528bb724dd09e404cdcb7cdbc33b203226#b12f5ac0052d9237edaacf8bc73366288bda6ce3"><strong>kineticsTools/MultiSiteCommon.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,7 +143,7 @@ class MultiSiteCommon(object):</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getContextMeans</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">meanVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="p">[(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pre</span><span class="p">):(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)].</span><span class="n" style="color: #333;">tostring</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;">ctx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="p">[(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pre</span><span class="p">):(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)].</span><span class="n" style="color: #333;">tostring</span><span class="p">()<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">decode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"ascii"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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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;">ctx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">contextMeanTable</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">meanVector</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">contextMeanTable</span><span class="p">[</span><span class="n" style="color: #333;">ctx</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/kineticstools/-/commit/cde481528bb724dd09e404cdcb7cdbc33b203226#3de438878d25828a21fc72e3e303cd3d341e4def"><strong>test/test_integration.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">@@ -13,10 +13,10 @@ EXPECTED_GFF = """\</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6307</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6307</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=56;context=CAGATTAGCACGCTGATGCGCATCAGCGACAAACTGGCGGG;IPDRatio=1.92</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6455</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6455</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">32</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=53;context=CCTGCAAGGACTGGATATGCTGATTCTTATTTCACCTGCGA;IPDRatio=1.78</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6512</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6512</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">32</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=55;context=GTAATCACAACTATCGATCAACTCATTCTCATTTTTTGCTA;IPDRatio=1.81</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m6A</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;identificationQv=5</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;identificationQv=4</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m6A</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6984</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;<span class="idiff left right">frac=0.627;fracLow=0.321;fracUp=0.911;</span>identificationQv=5</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;<span class="idiff left right">frac=1.000;fracLow=0.370;fracUp=1.000;</span>identificationQv=4</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20051</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20051</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">44</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=19;context=ACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGT;IPDRatio=2.54</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;identificationQv=9</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">m4C</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20296</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;<span class="idiff left right">frac=1.000;fracLow=0.379;fracUp=1.000;</span>identificationQv=9</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">Escherichia_coli_K12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">kinModCall</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">modified_base</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20449</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">20449</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">31</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage=18;context=TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGT;IPDRatio=2.49"""</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,6 +39,7 @@ class TestKineticsTools(PbIntegrationBase):</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"--csv"</span><span class="p">,</span> <span class="n" style="color: #333;">csv_out</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;">"--pvalue"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.001"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"--identify"</span><span class="p">,</span> <span class="s" style="color: #d14;">"m6A,m4C"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"--methylFraction"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"--reference"</span><span class="p">,</span> <span class="n" style="color: #333;">ref_set</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;">alignments</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="p">]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,6 +47,7 @@ class TestKineticsTools(PbIntegrationBase):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">gff_out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">csv_out</span><span class="p">)</span></span>
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48
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">gff_out</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;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">gff_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"rt"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gff</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gff</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">splitlines</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;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"##"</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(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">@@ -58,4 +60,4 @@ class TestKineticsTools(PbIntegrationBase):</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">csv_records</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">csv_records</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3222</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">csv_records</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33<span class="idiff left right">,,,</span>'</span></span></pre>
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