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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/gasic">Debian Med / gasic</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/commit/d26a8921928a6dbb153dfbe1afae524f2dad77f7">d26a8921</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T13:39:23Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">In run_mappers.py the executable mason from seqan-apps version 1.x was called. This is not available any more in seqan-apps 2.x and thus it was replaced by mason_simulator. Hope that's OK.
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/commit/84d34693475352cb5ba683ebf9645871f5ffd897">84d34693</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T13:39:46Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2to3 patch
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<strong><a href="https://salsa.debian.org/med-team/gasic/commit/0771aad1b4f633d48d1b5199869a37441a7c1b11">0771aad1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T13:53:32Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Packaging now uses Python3
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<h4>7 changed files:</h4>
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<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
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debian/README.Debian
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
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debian/patches/2to3.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#968c4691073d4f7c0f089a3fa020a3aefa835489">
debian/patches/use_seqan_mason.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/gasic/compare/636dd7caaf4830d4a7effd19b8b8344244a53989...0771aad1b4f633d48d1b5199869a37441a7c1b11#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gasic for Debian</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">================</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The run_mappers.py script contained code relying on SeQan 1. This was replaced</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">by SeQan 2 in Debian which does not contain the executable mason any more. The</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">original command:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o <out> <ref></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">was replaced by </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> mason_simulator illumina --illumina-read-length 10000 -o <out> <ref></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">It is not sure whether this provides comparable results. If you have a better</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">suggestion please write a bug report via</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> reportbug gasic</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 08 Oct 2019 15:01:07 +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/compare/636dd7caaf4830d4a7effd19b8b8344244a53989...0771aad1b4f633d48d1b5199869a37441a7c1b11#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gasic (0.0.r19-5) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #936582</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * In run_mappers.py the executable mason from seqan-apps version 1.x</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> was called. This is not available any more in seqan-apps 2.x and</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> thus it was replaced by mason_simulator. Hope that's OK.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 08 Oct 2019 15:01:07 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">gasic (0.0.r19-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * debhelper 11</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/gasic/compare/636dd7caaf4830d4a7effd19b8b8344244a53989...0771aad1b4f633d48d1b5199869a37441a7c1b11#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -6,7 +6,8 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-all-dev,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> bowtie2</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/gasic</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">@@ -16,12 +17,12 @@ Homepage: http://sourceforge.net/projects/gasic/</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Package: gasic</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> python-scipy,</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python-numpy,</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> python-biopython,</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> python-pysam,</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> python-matplotlib,</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-scipy,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-numpy,</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-biopython,</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pysam,</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-matplotlib,</span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> bowtie,</span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> bowtie2,</span>
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27
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> bwa,</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/gasic/compare/636dd7caaf4830d4a7effd19b8b8344244a53989...0771aad1b4f633d48d1b5199869a37441a7c1b11#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936582</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Tue, 08 Oct 2019 15:01:07 +0200</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/core/gasic.py</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/gasic.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span> def similarity_correction(sim, reads, N)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> A = sim</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> r = reads.astype(np.float) / N</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rng = range(len(reads))</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rng = list(range(len(reads)))</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # Now solve the optimization problem: min_c |Ac-r|^2 s.t. c_i >= 0 and 1-sum(c_i) >= 0</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # construct objective function</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -179,7 +179,7 @@</span> def bootstrap(reads, smat_raw, B, test_c</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # check if the calculated abundance is below the test abundance</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> fails[b,:] = corr[b,:] < test_c</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> p_values = np.mean(fails, axis=0)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> abundances = np.mean(corr, axis=0)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> variances = np.var(corr, axis=0)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/core/tools.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/tools.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -54,19 +54,19 @@</span> def read_names(filename):</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> def run_bowtie2(index, reads, out, param=""):</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> command = "bowtie2 -U {reads} -x {index} -S {samfile} {param} --local -M 0 ".format(reads=reads, index=index, samfile=out, param=param)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Executing:",command</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Executing:",command)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> os.system(command)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> return 1</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> def run_bowtie(index, reads, out, param=""):</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> command = "bowtie -S -p 2 -q -3 30 -v 2 {param} {index} {reads} > {samfile}".format(index=index, reads=reads, samfile=out, param=param)</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Executing:",command</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Executing:",command)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> os.system(command)</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> return 1</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> def run_bwa(index, reads, out, param=""):</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> command = "bwa aln {param} {index} {reads} > /tmp/res.sai".format(index=index, reads=reads, param=param)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Executing:",command</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Executing:",command)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> os.system(command)</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> # convert the bwa output to SAM and remove temporary file</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> command_sam = "bwa samse %s /tmp/res.sai %s > %s && rm /tmp/res.sai"%(index,reads,out)</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -75,7 +75,7 @@</span> def run_bwa(index, reads, out, param="")</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> def run_bwasw(index, reads, out, param=""):</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> command = "bwa bwasw {param} {index} {reads} > {samfile}".format(index=index, reads=reads, samfile=out, param=param)</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Executing:",command</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Executing:",command)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> os.system(command)</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> return 1</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -116,7 +116,7 @@</span> How to add your custom mapper</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> def run_mason_illumina(ref, out):</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> command = "mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o %s %s"%(out,ref)</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Executing:",command</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Executing:",command)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> os.system(command)</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> # remove the needless SAM file</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> command = "rm %s.sam"%out</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -125,7 +125,7 @@</span> def run_mason_illumina(ref, out):</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> def run_dwgsim(ref, out):</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> command = "dwgsim -c 2 -1 80 -2 0 -r 0 -y 0 -e 0.002 -N 100000 -f TACG %s %s"%(ref, out)</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Executing:",command</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Executing:",command)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> os.system(command)</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> # remove all additional files and rename reads file</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> command = "mv {out}.bfast.fastq {out} && rm {out}.bwa.read1.fastq && rm {out}.bwa.read2.fastq && rm {out}.mutations.txt".format(out=out)</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/correct_abundances.py</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/correct_abundances.py</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="p">@@ -55,10 +55,10 @@</span> def similarity_correction(names, smat_ra</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> p: p-value for the confidence, that the true abundance is above some threshold</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> """</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n--- GASiC correction\n"</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n--- GASiC correction\n")</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> # find out the number of reads</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> total = len( [1 for read in pysam.Samfile(sam_pattern%(names[0]), "r")] )</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " found %i reads"%total</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" found %i reads"%total)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> # initialize some arrays</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> # mapping information; mapped[i,j]=1 if read j was successfully mapped to i.</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="p">@@ -67,7 +67,7 @@</span> def similarity_correction(names, smat_ra</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> # total number of successfully mapped reads per reference</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> num_reads = np.zeros( (len(names),) )</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n--- Analyzing SAM files\n"</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n--- Analyzing SAM files\n")</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> # analyze the SAM files</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> for n_ind,nm in enumerate(names):</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> msg = " SAM file %i of %i"%(n_ind+1,len(names))</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="p">@@ -82,12 +82,12 @@</span> def similarity_correction(names, smat_ra</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> mapped[n_ind,:] = np.array([int(not rd.is_unmapped) for rd in sf])</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> num_reads[n_ind] = sum(mapped[n_ind,:])</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
</pre>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n\n--- Bootstrapping abundances\n"</span></span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\n--- Bootstrapping abundances\n")</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> # run similarity correction step</span>
</pre>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> p,corr,var = gasic.bootstrap(mapped, smat_raw, bootstrap_samples)</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> err = np.sqrt(var)</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> </span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\nDone estimating abundances\n"</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\nDone estimating abundances\n")</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> return total,num_reads,corr,err,p</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="p">@@ -170,7 +170,7 @@</span> See the provided LICENSE file or source</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> out = "{name}\t{mapped}\t{corr}\t{error}\t{pval}\n"</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> ofile.write(out.format(name=nm,mapped=num_reads[n_ind],corr=corr[n_ind]*total,error=err[n_ind]*total,pval=p[n_ind]))</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> ofile.close()</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "--- wrote results to", opt.out</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("--- wrote results to", opt.out)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> </span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> else:</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> parser.print_help()</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/create_matrix.py</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/create_matrix.py</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="p">@@ -63,14 +63,14 @@</span> def similarity_matrix_raw(names, ref_pat</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> os.makedirs(temp_dir)</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> n_seq = len(names)</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rng = range(n_seq)</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rng = list(range(n_seq))</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> # construct arrays with real file names from pattern</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> ref_files = [ ref_pattern%nm for nm in names ] # filenames of reference sequences</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="diff"> index_files = [ index_pattern%nm for nm in names ] # filenames of mapper index files</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> sim_files = [ temp_dir+'/'+nm+'.fastq' for nm in names ] # filenames of simulated read files</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n--- Simulating reads for each reference genome with %s\n"%simulator</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n--- Simulating reads for each reference genome with %s\n"%simulator)</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> # generate reads for every reference genome</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> for i in rng:</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> tools.run_simulator[simulator](ref_files[i], sim_files[i])</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="p">@@ -80,14 +80,14 @@</span> def similarity_matrix_raw(names, ref_pat</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> # and are stored in fastq format</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> num_reads = len( [ True for i in SeqIO.parse(sim_files[0],'fastq') ] )</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n--- Mapping simulated reads to reference genomes with %s\n"%mapper</span></span>
</pre>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n--- Mapping simulated reads to reference genomes with %s\n"%mapper)</span></span>
</pre>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> # map the reads of every reference to all references</span>
</pre>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> for i in rng:</span>
</pre>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> for j in rng:</span>
</pre>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> samfile = temp_dir+'/'+names[i]+'-'+names[j]+'.sam'</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> tools.run_mapper[mapper](index_files[j], sim_files[i], samfile)</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n--- Parsing SAM files\n"</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n--- Parsing SAM files\n")</span></span>
</pre>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> # parse SAM files</span>
</pre>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> mapped_reads = np.zeros((n_seq,n_seq, num_reads))</span>
</pre>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> for i in rng:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="p">@@ -102,7 +102,7 @@</span> def similarity_matrix_raw(names, ref_pat</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> samhandle = pysam.Samfile(samfile, "r")</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> mapped_reads[i,j,:] = np.array( [int(not read.is_unmapped) for read in samhandle] )</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> </span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n\nMatrix creation done\n"</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\nMatrix creation done\n")</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> return mapped_reads</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="p">@@ -152,7 +152,7 @@</span> See the provided LICENSE file or source</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> # save the similarity matrix</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> np.save(opt.out, smat)</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Wrote similarity matrix to",opt.out</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Wrote similarity matrix to",opt.out)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> else:</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> parser.print_help()</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> sys.exit(1)</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/run_mappers.py</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_mappers.py</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="p">@@ -76,9 +76,9 @@</span> READS: File containing the reads to be</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> for i in range(len(names)):</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> msg = "--- mapping reads with %s to %s"%(options.mapper, ref[i])</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print msg</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(msg)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> tools.run_mapper[options.mapper](ref[i], reads, out[i])</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\nMapping done.\n"</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\nMapping done.\n")</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> else:</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> parser.print_help()</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> sys.exit(1)</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/gasic/compare/636dd7caaf4830d4a7effd19b8b8344244a53989...0771aad1b4f633d48d1b5199869a37441a7c1b11#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2to3.patch</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_seqan_mason.patch</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_example_indentation.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/compare/636dd7caaf4830d4a7effd19b8b8344244a53989...0771aad1b4f633d48d1b5199869a37441a7c1b11#968c4691073d4f7c0f089a3fa020a3aefa835489"><strong>debian/patches/use_seqan_mason.patch</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">@@ -4,14 +4,21 @@ Description: since there is a name conflict with mason and the Debian package</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> mason is something else than the seqan tool, the code needs to be patched</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> to find /usr/lib/seqan/bin/mason</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="diff"></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">--- <span class="idiff left right">gasic.orig</span>/core/tools.py</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">gasic</span>/core/tools.py</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -115,7 +115,<span class="idiff left right">7 @@</span></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- <span class="idiff left right">a</span>/core/tools.py</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/core/tools.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -115,7 +115,<span class="idiff left">14 @@</span></span><span class="idiff right"> How to add your custom mapper</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> # to create a seperate caller function for every scenario.</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> def run_mason_illumina(ref, out):</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o %s %s"%(out,ref)</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "/usr/lib/seqan/bin/mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o %s %s"%(out,ref)</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> print "Executing:",command</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("""Original command with mason from SeQan 1 was</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o %s %s</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Please verify that the following call of mason_simulator fits your needs. If not</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+please use</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ reportbug gasic</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+to propose enhancements.</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+""" % (out,ref))</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "/usr/lib/seqan/bin/mason_simulator illumina --illumina-read-length 10000 -o %s %s"%(out,ref)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> print("Executing:",command)</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> os.system(command)</span>
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17
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> # remove the needless SAM file</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/compare/636dd7caaf4830d4a7effd19b8b8344244a53989...0771aad1b4f633d48d1b5199869a37441a7c1b11#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">@@ -3,7 +3,10 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> dh $@ --with python2</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> dh $@ --with python3</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">override_dh_python3:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh_python3 --shebang=/usr/bin/python3</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">get-orig-source:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> . debian/get-orig-source</span></pre>
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