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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/centrifuge">Debian Med / centrifuge</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/commit/7416efb072c89ab2e1091af8430d9353acb86024">7416efb0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:07:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/commit/a8203d6d0ebc237058e302107ccaf18e1c494652">a8203d6d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:07:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/commit/b96b8f0f14f96128a6e3563fcecaad1f746095df">b96b8f0f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:08:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/commit/3f21054b9f0ac8d37d7d57351f153c9eea043c37">3f21054b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:08:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/commit/199e8685814dfa6058681a856922574331255a80">199e8685</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:28:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use dh-python
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/commit/c8c350baaea33549d4b570992524275b688a4285">c8c350ba</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:31:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">centrifuge (1.0.3-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #936281</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * use dh-python</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"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 10 Sep 2019 08:20:22 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">centrifuge (1.0.3-2) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,10 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-sequence-python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> hisat2,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> jellyfish</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.0</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/centrifuge</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/centrifuge.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://ccb.jhu.edu/software/centrifuge/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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">@@ -15,7 +17,8 @@ Package: centrifuge</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> hisat2,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> jellyfish</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: rapid and memory-efficient system for classification of DNA sequences</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936281</span></span>
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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Tue, 10 Sep 2019 08:02:24 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/Makefile</span>
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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/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -364,11 +364,11 @@</span> centrifuge.bat:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> centrifuge-build.bat:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> echo "@echo off" > centrifuge-build.bat</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;">- echo "python %~dp0/centrifuge-build %*" >> centrifuge-build.bat</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;">+ echo "python3 %~dp0/centrifuge-build %*" >> centrifuge-build.bat</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"> centrifuge-inspect.bat:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> echo "@echo off" > centrifuge-inspect.bat</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "python %~dp0/centrifuge-inspect %*" >> centrifuge-inspect.bat</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "python3 %~dp0/centrifuge-inspect %*" >> centrifuge-inspect.bat</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> .PHONY: centrifuge-src</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/centrifuge-build</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/centrifuge-build</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> Copyright 2014, Daehwan Kim <infphilo@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/centrifuge-inspect</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/centrifuge-inspect</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </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"> Copyright 2014, Daehwan Kim <infphilo@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/evaluation/centrifuge_evaluate.py</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/evaluation/centrifuge_evaluate.py</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> import sys, os, subprocess, inspect</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> import platform, multiprocessing</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span> def read_taxonomy_tree(tax_file):</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> def compare_scm(centrifuge_out, true_out, taxonomy_tree, rank):</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> ancestors = set()</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for tax_id in taxonomy_tree.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for tax_id in list(taxonomy_tree.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> if tax_id in ancestors:</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> continue</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> while True:</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -106,7 +106,7 @@</span> def compare_scm(centrifuge_out, true_out</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> unclassified += 1</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> raw_unique_classified = 0</span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for value in db_dic.values():</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for value in list(db_dic.values()):</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> if len(value) == 1:</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> raw_unique_classified += 1</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> return classified, unique_classified, unclassified, len(db_dic), raw_unique_classified</span>
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<td class="diff-line-num new new_line" data-linenumber="64" 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">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -152,7 +152,7 @@</span> def compare_abundance(centrifuge_out, tr</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> if tax_id in db_dic:</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> SSR += (abundance - db_dic[tax_id]) ** 2;</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> if debug:</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\t\t{:<10}: {:.6} vs. {:.6} (truth vs. centrifuge)".format(tax_id, abundance, db_dic[tax_id])</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\t\t{:<10}: {:.6} vs. {:.6} (truth vs. centrifuge)".format(tax_id, abundance, db_dic[tax_id]), file=sys.stderr)</span></span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> else:</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> SSR += (abundance) ** 2</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -179,7 +179,7 @@</span> def sql_execute(sql_db, sql_query):</span>
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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> """</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> def create_sql_db(sql_db):</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> if os.path.exists(sql_db):</span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, sql_db, "already exists!"</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(sql_db, "already exists!", file=sys.stderr)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> return</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> columns = [</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -316,7 +316,7 @@</span> def evaluate(index_base,</span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> os.mkdir(index_path)</span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> index_fnames = ["%s/%s.%d.cf" % (index_path, index_base, i+1) for i in range(3)]</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> if not check_files(index_fnames):</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Downloading indexes: %s" % ("index")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Downloading indexes: %s" % ("index"), file=sys.stderr)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> os.system("cd %s; wget ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/%s.tar.gz; tar xvzf %s.tar.gz; rm %s.tar.gz; ln -s %s/%s* .; cd -" % \</span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> (index_path, index_base, index_base, index_base, index_base, index_base))</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> assert check_files(index_fnames) </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="p">@@ -356,7 +356,7 @@</span> def evaluate(index_base,</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> scm_fname = "%s/%s.scm" % (read_path, read_base)</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> read_fnames = [read1_fname, read2_fname, truth_fname, scm_fname]</span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> if not check_files(read_fnames):</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Simulating reads %s_1.fq %s_2.fq ..." % (read_base, read_base)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Simulating reads %s_1.fq %s_2.fq ..." % (read_base, read_base), file=sys.stderr)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> centrifuge_simulate = os.path.join(path_base, "centrifuge_simulate_reads.py")</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> simulate_cmd = [centrifuge_simulate,</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> "--num-fragment", str(num_fragment)]</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="p">@@ -377,11 +377,11 @@</span> def evaluate(index_base,</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> else:</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> base_fname = read_base + "_single"</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Database: %s" % (index_base)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Database: %s" % (index_base), file=sys.stderr)</span></span>
</pre>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> if paired:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t%d million pairs" % (num_fragment / 1000000)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t%d million pairs" % (num_fragment / 1000000), file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t%d million reads" % (num_fragment / 1000000)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t%d million reads" % (num_fragment / 1000000), file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> program_bin_base = "%s/.." % path_base</span>
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<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> def get_program_version(program, version):</span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -428,7 +428,7 @@</span> def evaluate(index_base,</span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> if version:</span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> program_name += ("_%s" % version)</span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t%s\t%s" % (program_name, str(datetime.now()))</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t%s\t%s" % (program_name, str(datetime.now())), file=sys.stderr)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> if paired:</span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> program_dir = program_name + "_paired"</span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> else:</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="p">@@ -449,7 +449,7 @@</span> def evaluate(index_base,</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> program_cmd = get_program_cmd(program, version, read1_fname, read2_fname, out_fname)</span>
</pre>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> start_time = datetime.now()</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> if verbose:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t", start_time, " ".join(program_cmd)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t", start_time, " ".join(program_cmd), file=sys.stderr)</span></span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> if program in ["centrifuge"]:</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> proc = subprocess.Popen(program_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -462,7 +462,7 @@</span> def evaluate(index_base,</span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> if duration < 0.1:</span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> duration = 0.1</span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> if verbose:</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"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t", finish_time, "finished:", duration </span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t", finish_time, "finished:", duration, file=sys.stderr) </span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> results = {"strain" : [0, 0, 0],</span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> "species" : [0, 0, 0],</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="p">@@ -484,21 +484,21 @@</span> def evaluate(index_base,</span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> # if rank == "strain":</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> # assert num_cases == num_fragment</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t%s" % rank</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\n\t\t\tfor uniquely classified ",</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
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("\t\t%s" % rank, file=sys.stderr)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases), file=sys.stderr)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified), file=sys.stderr)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\t\t\tfor uniquely classified ", end=' ', file=sys.stderr)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> if paired:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "pairs"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("pairs", file=sys.stderr)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> else:</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "reads"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("reads", file=sys.stderr)</span></span>
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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="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases), file=sys.stderr)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified), file=sys.stderr)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> # Calculate sum of squared residuals in abundance</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> if rank == "strain":</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> abundance_SSR = compare_abundance("centrifuge_report.tsv", truth_fname, taxonomy_tree, debug)</span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\tsum of squared residuals in abundance: {}".format(abundance_SSR)</span></span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\tsum of squared residuals in abundance: {}".format(abundance_SSR), file=sys.stderr)</span></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"> if runtime_only:</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> os.chdir("..")</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/evaluation/centrifuge_simulate_reads.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/evaluation/centrifuge_simulate_reads.py</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> # Copyright 2015, Daehwan Kim <infphilo@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="p">@@ -156,7 +156,7 @@</span> def read_transcript(genomes_seq, gtf_fil</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> transcripts[transcript_id][2].append([left, right])</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> # Sort exons and merge where separating introns are <=5 bps</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for tran, [chr, strand, exons] in transcripts.items():</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for tran, [chr, strand, exons] in list(transcripts.items()):</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> exons.sort()</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> tmp_exons = [exons[0]]</span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> for i in range(1, len(exons)):</span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="p">@@ -167,7 +167,7 @@</span> def read_transcript(genomes_seq, gtf_fil</span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> transcripts[tran] = [chr, strand, tmp_exons]</span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> tmp_transcripts = {}</span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for tran, [chr, strand, exons] in transcripts.items():</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for tran, [chr, strand, exons] in list(transcripts.items()):</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> exon_lens = [e[1] - e[0] + 1 for e in exons]</span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> transcript_len = sum(exon_lens)</span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> if transcript_len >= frag_len:</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="p">@@ -444,8 +444,8 @@</span> def getSamAlignment(dna, exons, genome_s</span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> MD += ("{}".format(MD_match_len))</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> if len(read_seq) != read_len:</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "read length differs:", len(read_seq), "vs.", read_len</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, pos, "".join(cigars), cigar_descs, MD, XM, NM, Zs</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("read length differs:", len(read_seq), "vs.", read_len, file=sys.stderr)</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(pos, "".join(cigars), cigar_descs, MD, XM, NM, Zs, file=sys.stderr)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> assert False</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> </span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> return pos, cigars, cigar_descs, MD, XM, NM, Zs, read_seq</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="p">@@ -575,8 +575,8 @@</span> def samRepOk(genome_seq, read_seq, chr,</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> tMD += ("{}".format(match_len))</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> if tMD != MD or tXM != XM or tNM != NM or XM > max_mismatch or XM != NM:</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, chr, pos, cigar, MD, XM, NM, Zs</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, tMD, tXM, tNM</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(chr, pos, cigar, MD, XM, NM, Zs, file=sys.stderr)</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(tMD, tXM, tNM, file=sys.stderr)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> assert False</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -631,7 +631,7 @@</span> def simulate_reads(index_fname, base_fna</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> # Read genome sequences into memory</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> genomes_fname = index_fname + ".fa"</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> if not os.path.exists(genomes_fname):</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Extracting genomes from Centrifuge index to %s, which may take a few hours ..." % (genomes_fname)</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Extracting genomes from Centrifuge index to %s, which may take a few hours ..." % (genomes_fname), file=sys.stderr)</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> extract_cmd = [centrifuge_inspect,</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> index_fname]</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> extract_proc = subprocess.Popen(extract_cmd, stdout=open(genomes_fname, 'w'))</span>
</pre>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="p">@@ -660,15 +660,15 @@</span> def simulate_reads(index_fname, base_fna</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> assert num_frag == sum(expr_profile)</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> if dna:</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- genome_ids = genome_seqs.keys()</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ genome_ids = list(genome_seqs.keys())</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- transcript_ids = transcripts.keys()</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ transcript_ids = list(transcripts.keys())</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> random.shuffle(transcript_ids)</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> assert len(transcript_ids) >= len(expr_profile)</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> # Truth table</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> truth_file = open(base_fname + ".truth", "w")</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> truth_file, "taxID\tgenomeLen\tnumReads\tabundance\tname"</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("taxID\tgenomeLen\tnumReads\tabundance\tname", file=truth_file)</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> truth_list = []</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> normalized_sum = 0.0</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> debug_num_frag = 0</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="p">@@ -695,19 +695,19 @@</span> def simulate_reads(index_fname, base_fna</span>
</pre>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> if can_tax_id in names:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> name = names[can_tax_id]</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> abundance = raw_abundance / genome_len / normalized_sum</span>
</pre>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> truth_file, "{}\t{}\t{}\t{:.6}\t{}".format(tax_id, genome_len, t_num_frags, abundance, name)</span></span>
</pre>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("{}\t{}\t{}\t{:.6}\t{}".format(tax_id, genome_len, t_num_frags, abundance, name), file=truth_file)</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> truth_file.close()</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> </span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> # Sequence Classification Map (SCM) - something I made up ;-)</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> scm_file = open(base_fname + ".scm", "w")</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> </span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> # Write SCM header</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> scm_file, "@HD\tVN:1.0\tSO:unsorted"</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for tax_id in genome_seqs.keys():</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@HD\tVN:1.0\tSO:unsorted", file=scm_file)</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for tax_id in list(genome_seqs.keys()):</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> name = ""</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> if tax_id in names:</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> name = names[tax_id]</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> scm_file, "@SQ\tTID:%s\tSN:%s\tLN:%d" % (tax_id, name, len(genome_seqs[tax_id]))</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@SQ\tTID:%s\tSN:%s\tLN:%d" % (tax_id, name, len(genome_seqs[tax_id])), file=scm_file)</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> </span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> read_file = open(base_fname + "_1.fa", "w")</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> if paired_end:</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="p">@@ -718,11 +718,11 @@</span> def simulate_reads(index_fname, base_fna</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> t_num_frags = expr_profile[t]</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> if dna:</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> tax_id = genome_ids[t]</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "TaxID: %s, num fragments: %d" % (tax_id, t_num_frags)</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("TaxID: %s, num fragments: %d" % (tax_id, t_num_frags), file=sys.stderr)</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> transcript_id = transcript_ids[t]</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> chr, strand, transcript_len, exons = transcripts[transcript_id]</span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, transcript_id, t_num_frags</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(transcript_id, t_num_frags, file=sys.stderr)</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> genome_seq = genome_seqs[tax_id]</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> genome_len = len(genome_seq)</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="p">@@ -763,14 +763,14 @@</span> def simulate_reads(index_fname, base_fna</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> XS = "\tXS:A:{}".format(strand)</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> TI = "\tTI:Z:{}".format(transcript_id) </span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> read_file, ">{}".format(cur_read_id)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> read_file, read_seq</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(">{}".format(cur_read_id), file=read_file)</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(read_seq, file=read_file)</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> output = "{}\t{}\t{}\t{}\tNM:i:{}\tMD:Z:{}".format(cur_read_id, tax_id, pos + 1, cigar_str, NM, MD)</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> if paired_end:</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> read2_file, ">{}".format(cur_read_id)</span></span>
</pre>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> read2_file, reverse_complement(read2_seq)</span></span>
</pre>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(">{}".format(cur_read_id), file=read2_file)</span></span>
</pre>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(reverse_complement(read2_seq), file=read2_file)</span></span>
</pre>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> output += "\t{}\t{}\tNM2:i:{}\tMD2:Z:{}".format(pos2 + 1, cigar2_str, NM2, MD2)</span>
</pre>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> scm_file, output</span></span>
</pre>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(output, file=scm_file)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> cur_read_id += 1</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="p">@@ -865,7 +865,7 @@</span> if __name__ == '__main__':</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> parser.print_help()</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> exit(1)</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> if not args.dna:</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Error: --rna is not implemented."</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Error: --rna is not implemented.", file=sys.stderr)</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> exit(1)</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> # if args.dna:</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> # args.expr_profile = "constant"</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/evaluation/test/centrifuge_evaluate_mason.py</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/evaluation/test/centrifuge_evaluate_mason.py</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> import sys, os, subprocess, inspect</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> import platform, multiprocessing</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="p">@@ -27,7 +27,7 @@</span> def compare_scm(centrifuge_out, true_out</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> higher_ranked = {}</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> </span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> ancestors = set()</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for tax_id in taxonomy_tree.keys():</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for tax_id in list(taxonomy_tree.keys()):</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> if tax_id in ancestors:</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> continue</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> while True:</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="p">@@ -82,7 +82,7 @@</span> def compare_scm(centrifuge_out, true_out</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> </span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> fields = line.strip().split('\t')</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> if len(fields) != 3:</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Warning: %s missing" % (line.strip())</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Warning: %s missing" % (line.strip()), file=sys.stderr)</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> continue</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> read_name, tax_id = fields[1:3] </span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> # Traverse up taxonomy tree to match the given rank parameter</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="p">@@ -117,7 +117,7 @@</span> def compare_scm(centrifuge_out, true_out</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> # print read_name</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> </span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> raw_unique_classified = 0</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for read_name, maps in db_dic.items():</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for read_name, maps in list(db_dic.items()):</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> if len(maps) == 1 and read_name not in higher_ranked:</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> raw_unique_classified += 1</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> return classified, unique_classified, unclassified, len(db_dic), raw_unique_classified</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="p">@@ -184,7 +184,7 @@</span> def evaluate(index_base,</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> read_fname]</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> </span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> if verbose:</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, ' '.join(centrifuge_cmd)</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(' '.join(centrifuge_cmd), file=sys.stderr)</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> </span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> out_fname = "centrifuge.output"</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> proc = subprocess.Popen(centrifuge_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="p">@@ -208,12 +208,12 @@</span> def evaluate(index_base,</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> # if rank == "strain":</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> # assert num_cases == num_fragment</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> </span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t%s" % rank</span></span>
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<td class="diff-line-num new new_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified)</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\n\t\t\tfor uniquely classified "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="368" 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">
368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases)</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified)</span></span>
</pre>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t%s" % rank, file=sys.stderr)</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases), file=sys.stderr)</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified), file=sys.stderr)</span></span>
</pre>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\t\t\tfor uniquely classified ", file=sys.stderr)</span></span>
</pre>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases), file=sys.stderr)</span></span>
</pre>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified), file=sys.stderr)</span></span>
</pre>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> </span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> # Calculate sum of squared residuals in abundance</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> """</span>
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<td class="diff-line-num new new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="p">@@ -252,12 +252,12 @@</span> def evaluate(index_base,</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> if rank_taxID not in true_abundance:</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> true_abundance[rank_taxID] = 0.0</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> true_abundance[rank_taxID] += (reads / float(genomeSize))</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for taxID, reads in true_abundance.items():</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for taxID, reads in list(true_abundance.items()):</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> true_abundance[taxID] /= total_sum</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> </span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "number of genomes:", num_genomes</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "number of species:", num_species</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "number of uniq species:", len(true_abundance)</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("number of genomes:", num_genomes, file=sys.stderr)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("number of species:", num_species, file=sys.stderr)</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("number of uniq species:", len(true_abundance), file=sys.stderr)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> </span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> read_fname = "centrifuge_data/bacteria_sim10M/bacteria_sim10M.fa"</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> summary_fname = "centrifuge.summary"</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="p">@@ -271,14 +271,14 @@</span> def evaluate(index_base,</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> read_fname]</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> </span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> if verbose:</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, ' '.join(centrifuge_cmd)</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(' '.join(centrifuge_cmd), file=sys.stderr)</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> </span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> out_fname = "centrifuge.output"</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> proc = subprocess.Popen(centrifuge_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> proc.communicate()</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> </span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> calc_abundance = {}</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for taxID in true_abundance.keys():</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for taxID in list(true_abundance.keys()):</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> calc_abundance[taxID] = 0.0</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> first = True</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> for line in open(summary_fname):</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="p">@@ -296,12 +296,12 @@</span> def evaluate(index_base,</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> """</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> </span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> abundance_file = open("abundance.cmp", 'w')</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> abundance_file, "taxID\ttrue\tcalc\trank"</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("taxID\ttrue\tcalc\trank", file=abundance_file)</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> for rank in ranks:</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> if rank == "strain":</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> continue</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> true_abundance_rank, calc_abundance_rank = {}, {}</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for taxID in true_abundance.keys():</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for taxID in list(true_abundance.keys()):</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> assert taxID in calc_abundance</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> rank_taxID = taxID</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> while True:</span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="p">@@ -322,11 +322,11 @@</span> def evaluate(index_base,</span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> calc_abundance_rank[rank_taxID] += calc_abundance[taxID]</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> ssr = 0.0 # Sum of Squared Residuals</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for taxID in true_abundance_rank.keys():</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for taxID in list(true_abundance_rank.keys()):</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> assert taxID in calc_abundance_rank</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> ssr += (true_abundance_rank[taxID] - calc_abundance_rank[taxID]) ** 2</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> abundance_file, "%s\t%.6f\t%.6f\t%s" % (taxID, true_abundance_rank[taxID], calc_abundance_rank[taxID], rank)</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "%s) Sum of squared residuals: %.6f" % (rank, ssr)</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s\t%.6f\t%.6f\t%s" % (taxID, true_abundance_rank[taxID], calc_abundance_rank[taxID], rank), file=abundance_file)</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s) Sum of squared residuals: %.6f" % (rank, ssr), file=sys.stderr)</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> abundance_file.close()</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,3 +3,4 @@ fix_auto_ptr_usage_in_gcc-7.patch</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">0003-Fix-make-install-DESTDIR.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">hardening.patch</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="plaintext">no_msse2.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285#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">@@ -9,7 +9,7 @@ include /usr/share/dpkg/default.mk</td>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">export POPCNT_CAPABILITY=0</span>
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11
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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"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with python3</span></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">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh_auto_install -- prefix=/usr/lib/centrifuge</span>
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