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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/arden">Debian Med / arden</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/arden/commit/b1341df94f9f8721592c156030f1d43ed318e365">b1341df9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T07:53:11Z</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/arden/commit/69d081d5de7e4ddc5bbec507e10fad7c145ec4aa">69d081d5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T07:53:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Packaging with Python3 modules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/arden/commit/38f798494f4d989e6754004a6448d044750b14dd">38f79849</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T07:56:21Z</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/arden/commit/b3d7525af6587995fe7bdebc27150659c8e55a6f">b3d7525a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T07:56:34Z</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/arden/commit/a57e711a89edf2e9d77524c8551959a575a7e0bd">a57e711a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-13T08:09:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix incomplete 2to3 patch
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#85f404a0760e49ec237056c4b1f037904e9e3a67">
<span class="new-file">
+
debian/patches/2to3_new.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/arden/compare/8d01d92569c89adbe2002dd069df55a944d28c09...a57e711a89edf2e9d77524c8551959a575a7e0bd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<td class="diff-line-num new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">arden (1.0-5) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<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"> [ Jelmer Vernooij ]</span>
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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Use secure copyright file specification URI.</span>
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<td class="diff-line-num new_line" data-linenumber="5" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Jelmer Vernooij <jelmer@debian.org> Tue, 16 Oct 2018 22:13:51 +0000</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"> [ Andreas Tille ]</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 2to3 to port to Python3</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"> * debhelper-compat 12</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"> * Standards-Version: 4.4.0</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 new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 13 Sep 2019 09:51:05 +0200</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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">arden (1.0-4) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/arden/compare/8d01d92569c89adbe2002dd069df55a944d28c09...a57e711a89edf2e9d77524c8551959a575a7e0bd#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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1
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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/arden/compare/8d01d92569c89adbe2002dd069df55a944d28c09...a57e711a89edf2e9d77524c8551959a575a7e0bd#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 +3,10 @@ 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<span class="idiff left right"> (>= 11~</span>),</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python-all</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.5</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-all</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/arden</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/arden.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: http://sourceforge.net/projects/arden/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -14,11 +14,11 @@ Homepage: http://sourceforge.net/projects/arden/</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Package: arden</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> python-scipy,</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> python-numpy,</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> python-htseq,</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python-matplotlib</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-scipy,</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-numpy,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-htseq,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-matplotlib</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Description: specificity control for read alignments using an artificial reference</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ARDEN (Artificial Reference Driven Estimation of false positives in NGS</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> data) is a novel benchmark that estimates error rates based on real</span>
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<li id="85f404a0760e49ec237056c4b1f037904e9e3a67">
<a href="https://salsa.debian.org/med-team/arden/compare/8d01d92569c89adbe2002dd069df55a944d28c09...a57e711a89edf2e9d77524c8551959a575a7e0bd#85f404a0760e49ec237056c4b1f037904e9e3a67"><strong>debian/patches/2to3_new.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">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Fri, 13 Sep 2019 09:51:05 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/README</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span> Table of Contents</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 4. Installation </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> ---------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ARDEN is a collection of python scripts and therefore needs no installation.</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ARDEN is a collection of python3 scripts and therefore needs no installation.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> It was built and tested on a Linux platform. However, for convenient access it</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> is recommended to do the following adjustments to your environment variables:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> export PATH = $PATH:/path/to/ARDEN</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -51,9 +51,10 @@</span> Table of Contents</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> 5. Dependencies </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> ---------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> ARDEN makes use of the following python packages, that are all mandatory</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (ARDEN was developed under Python 2.7):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (ARDEN was developed under Python 2.7 but ported to Python3 by the Debian</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Med team):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * Python 2.7, http://www.python.org/</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Python 3.7, http://www.python.org/</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> * NumPy 1.6.1, http://numpy.scipy.org/</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> * SciPy 0.10.0, http://www.scipy.org/</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> * HTSeq 0.5.3p9, https://pypi.python.org/pypi/HTSeq</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/arden-analyze</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/arden-analyze</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> Created on Thu Aug 18 2012</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"><span class="p">@@ -64,7 +64,7 @@</span> def TestFiles(input):</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> fobj.close()</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> except IOError:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> # nope --> error</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;">- print "error opening file %s. Does it exist?" % controlDic["mapper"][mapper][0][0]</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;">+ print("error opening file %s. Does it exist?" % controlDic["mapper"][mapper][0][0])</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> error =1</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> # do the same for the artificial reference mappings</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -74,7 +74,7 @@</span> def TestFiles(input):</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> fobj = open(artificial,"r")</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> fobj.close()</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> except IOError:</span>
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<td class="diff-line-num new new_line" data-linenumber="50" 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">
50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "error opening file %s. Does it exist?" % artificial</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("error opening file %s. Does it exist?" % artificial)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> error =1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> return(error)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="55" 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">
55
</td>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -118,20 +118,20 @@</span> def main():</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> controlDic = AM.readInput(input)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> print("#######################################################################################")</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Input Settings:")</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="60" 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">
60
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Inputfile:\t%s" % input)</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Outputpath:\t%s" % outpath)</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="62" 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">
62
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Reads:\t%s" % controlDic["fastqfile"])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("UseInternalRank:\t%s" % UseInternalRank)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Phred:\t%s" % phred)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Input Settings:")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Inputfile:\t%s" % input)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Outputpath:\t%s" % outpath)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reads:\t%s" % controlDic["fastqfile"])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("UseInternalRank:\t%s" % UseInternalRank)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Phred:\t%s" % phred)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> print("#######################################################################################")</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("\r\nStart...")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\r\nStart...")</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<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"> error = TestFiles(input)</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> if error == 1:</span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Program aborted. Check your inputfiles!"</span></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="gi" style="color: #000; background-color: #dfd;">+ print("Program aborted. Check your inputfiles!")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> sys.exit()</span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Inputfiles checked successfully."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Inputfiles checked successfully.")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </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"> # check if output dir exists; else create output </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"> if not os.path.exists(os.path.dirname(outpath)):</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -164,8 +164,8 @@</span> def main():</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> #### looping #####</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"><span class="gd" style="color: #000; background-color: #fdd;">- print ("########Progress (analysis):########")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Mapper\t\tOutputfile\t\tOverallAlignments (TP/FP)\t\t Time")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("########Progress (analysis):########")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Mapper\t\tOutputfile\t\tOverallAlignments (TP/FP)\t\t Time")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> for mapper in controlDic["mapper"].keys():</span>
</pre>
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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"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="p">@@ -175,7 +175,7 @@</span> def main():</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"> # set refname</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> refname = controlDic["mapper"][mapper][0][0].split("/")[-1]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("%s" %mapper.upper()),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%s" %mapper.upper()),</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> if UseInternalRank == 1:</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"> rankDic = AM.GetOrderDictionary(controlDic["mapper"][mapper][0][0])</span>
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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="p">@@ -199,17 +199,17 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> resultdic["mreads"][outfile] = MappedReads</span>
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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"> resultdic["id"].append(outfile)</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>
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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"><span class="gd" style="color: #000; background-color: #fdd;">- print (outfile),</span></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 ("\t%0.2f (%0.2f/%0.2f)" %(tp+fp,tp,fp)),</span></span>
</pre>
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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="gd" style="color: #000; background-color: #fdd;">- print ("\t%0.2f sec." %(end-start))</span></span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(outfile),</span></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"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t%0.2f (%0.2f/%0.2f)" %(tp+fp,tp,fp)),</span></span>
</pre>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t%0.2f sec." %(end-start))</span></span>
</pre>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> ##################################################################################################################################</span>
</pre>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
</pre>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span>
</pre>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> # start evaluation process. SAM files are not getting touched anymore</span>
</pre>
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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 ("\r\n########Progress (evaluation):########") </span></span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Mapper\tTP\tFP\tTime")</span></span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\r\n########Progress (evaluation):########")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Mapper\tTP\tFP\tTime")</span></span>
</pre>
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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"> for resultfile in resultdic["id"]:</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print resultfile.split("_")[0],</span></span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(resultfile.split("_")[0],)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> </span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> #do sme name generation for this iteration</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> prefix = outpath+resultfile.split(".")[0]</span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="p">@@ -222,8 +222,8 @@</span> def main():</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> tp =[i for i in dataArray if i.mr[0] ==1]</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> fp =[i for i in dataArray if i.mr[0] ==0]</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("\t %d" % resultdic["alngts"][resultfile][0]), # TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("\t %d" % resultdic["alngts"][resultfile][1]), # FP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t %d" % resultdic["alngts"][resultfile][0]), # TP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t %d" % resultdic["alngts"][resultfile][1]), # FP</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> start = time.time()</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> #try:</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"><span class="p">@@ -233,7 +233,7 @@</span> def main():</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> </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"> end = time.time()</span>
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<td class="diff-line-num new new_line" data-linenumber="144" 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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("\t%0.2f" %(end-start))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t%0.2f" %(end-start))</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> </span>
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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"> # prepare labels and names for plotting the data</span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> ids =[i for i in resultdic['id']]</span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="p">@@ -273,5 +273,5 @@</span> if __name__ == "__main__":</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> a = time.time()</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> main()</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> b = time.time()</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Finished!")</span></span>
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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"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Done in %0.2f seconds!" % (b-a))</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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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("Finished!")</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Done in %0.2f seconds!" % (b-a))</span></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;">--- a/arden-create</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/arden-create</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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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;">+#!/usr/bin/python3</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> """</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> Created 2012</span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> Main script for generating an artificial reference genome. It calls various modules from core.</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="p">@@ -64,8 +64,8 @@</span> def printExample():</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> </span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> """</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> print("\r\nEXAMPLES:\r\n")</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Here are 3 simple examples with all kinds of different settings. The general input scheme is:")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("usage: python createAR.py [options] [OUTPUTFOLDER] [INPUT FASTA])\r\n")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Here are 3 simple examples with all kinds of different settings. The general input scheme is:")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: python createAR.py [options] [OUTPUTFOLDER] [INPUT FASTA])\r\n")</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"> print("Case 1:")</span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> print("\t -f random.fasta (inputfile)")</span>
</pre>
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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"> print("\t -p /home/ART (outputpath)")</span>
</pre>
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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="p">@@ -150,7 +150,7 @@</span> def Create():</span>
</pre>
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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>
</pre>
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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"> # adjust to complete path</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> #outputpath = os.path.abspath(outputpath+"/")</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print outputpath</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(outputpath)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> # create output directory if necessary</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> if not os.path.exists(os.path.dirname(outputpath)):</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="p">@@ -170,7 +170,7 @@</span> def Create():</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> print("rev:\t\t" + str(rev))</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
</td>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> print("random:\t\t" + str(random))</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
</td>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> print("###################################################")</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="190" 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">
190
</td>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("\r\nStart:")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\r\nStart:")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
</td>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> print("\tReading DNA...")</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="193" 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">
193
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> Reference = RAW.readdna(inputpath)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="194" 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">
194
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="p">@@ -249,8 +249,8 @@</span> def Create():</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> a = time.time()</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> Create()</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> b = time.time()</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
</td>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print ("Finished!")</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print ("Processed %d bases in %f seconds!" % (bases,b-a))</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("Finished!")</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("Processed %d bases in %f seconds!" % (bases,b-a))</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> </span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> </span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/arden-filter</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/arden-filter</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> """</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> Script for filtering alignments with deficient properties (rqs,gaps, mismatches). The script generates a new .SAM file from the input SAM file, where only alignments are</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> contained that fulfill certain quality thresholds.</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="p">@@ -82,9 +82,9 @@</span> def writeFilteredReads(iddic,fastqfile,f</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> </span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> counter+=1</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print fastqoutput</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (str(len(iddic)) + " ids" )</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (str(counter) + " reads to file written..." )</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print(fastqoutput)</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(str(len(iddic)) + " ids" )</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(str(counter) + " reads to file written..." )</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> fastqoutput.close()</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="226" 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">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> def getMisGapRQ(alngt):</span>
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<td class="diff-line-num new new_line" data-linenumber="227" 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">
227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="p">@@ -174,16 +174,16 @@</span> def FilterSAM(samfile,MISM,GAPS,RQ,fsam)</span>
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<td class="diff-line-num new new_line" data-linenumber="228" 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">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> counter2 +=1</span>
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<td class="diff-line-num new new_line" data-linenumber="230" 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">
230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="231" 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">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print ("%s\t%s\t%s\r\n" % (rqs,gaps,mismatches))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="232" 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">
232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print("%s\t%s\t%s\r\n" % (rqs,gaps,mismatches))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="233" 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">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> </span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> #test.write("%s\t%s\t%s\r\n" % (rqs,gaps,mismatches))</span>
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<td class="diff-line-num new new_line" data-linenumber="235" 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">
235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("PASSED\tREMOVED\tOVERALL")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="237" 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">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print counter1,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="238" 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">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t",</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print counter2,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="240" 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">
240
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t",</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print counter1+counter2</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="242" 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">
242
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("PASSED\tREMOVED\tOVERALL")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="243" 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">
243
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(counter1,)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="244" 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">
244
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t",)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="245" 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">
245
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(counter2,)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t",)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(counter1+counter2)</span></span>
</pre>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="249" 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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="250" 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">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> def readHeader(samfile):</span>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="p">@@ -256,7 +256,7 @@</span> def filter():</span>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> print("MM <=:\t\t" + str(mismatches))</span>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> print("GAPS <=:\t" + str(gaps))</span>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> print("###################################################")</span>
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<td class="diff-line-num new new_line" data-linenumber="255" 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">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("Start...")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Start...")</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> a = time.time() </span>
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<td class="diff-line-num new new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> header = readHeader(input)</span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
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"><span class="p">@@ -269,7 +269,7 @@</span> def filter():</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> # close current Readfile</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> fsam.close()</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> b = time.time()</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("DONE in %f seconds!" %(b-a))</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("DONE in %f seconds!" %(b-a))</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> </span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> if __name__ == "__main__":</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/core/AnalyseMapping.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/AnalyseMapping.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" 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="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> """ This script is used to evalulate the mapping results """</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> </span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> import HTSeq</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;">-import cPickle as pickle</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;">+import pickle as pickle</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> import numpy as np</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> import time</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> import sys</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> def savepickle(dictionaary, outputname):</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> </span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> def loadpickle(inputname):</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> dictionary = pickle.load(open(inputname + ".p"))</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Loaded " + inputname + ".pickle!")</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Loaded " + inputname + ".pickle!"))</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> return (dictionary)</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> </span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> </span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="p">@@ -201,7 +201,7 @@</span> def GetOrderDictionary(referenceSAM):</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> i += 1</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> </span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> index = 0</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k in xrange(i, len(readnames)):</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k in range(i, len(readnames)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> if readnames[k] in internalDic:</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> pass</span>
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<td class="diff-line-num new new_line" data-linenumber="299" 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="LC299" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="p">@@ -331,10 +331,10 @@</span> def CompareAlignments(reflist, artlist,f</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> file.write(RefRead.toStrNoMem("ref"))</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> </span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> # add 1 for every alignment from the artificial that is found on the reference</span>
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<td class="diff-line-num new new_line" data-linenumber="304" 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">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, artlen):</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, artlen):</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> # bool which decides if artificial in reference hit</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> ArtInRef = 0</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(0,reflen):</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(0,reflen):</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> if artlist[i].start == reflist[j].start and artlist[i].end == reflist[j].end:</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> ArtInRef = 1</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> break</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="p">@@ -455,7 +455,7 @@</span> def ReadSAMnoMem(ref, art, output, compa</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> while 1:</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> i += 1</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> if i == 100000:</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t\t%f" % (time.time() - start),</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t\t%f" % (time.time() - start), end=' ')</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> </span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> RefReadRank,ArtReadRank = getRanks(RefRead,ArtRead,rankdic)</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> </span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="p">@@ -465,7 +465,7 @@</span> def ReadSAMnoMem(ref, art, output, compa</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> #while (RefRead[0].id > ArtRead[0].id and hasNextLine != 0):</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> while (RefReadRank > ArtReadRank and hasNextLine != 0):</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> # in case of multiple hits, set all mr variables to 0 and get the best alignment</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for l in xrange(0, len(ArtRead)):</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for l in range(0, len(ArtRead)):</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> ArtRead[l].mr = [0]</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> </span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> # write FP to file</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="p">@@ -541,7 +541,7 @@</span> def ReadSAMnoMem(ref, art, output, compa</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> while (RefReadRank > ArtReadRank and hasNextLine != 0):</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> MappedReads+=1</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> # in case of multiple hits, set all mr variables to 0 and get the best alignment</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for l in xrange(0, len(ArtRead)):</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for l in range(0, len(ArtRead)):</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> ArtRead[l].mr = [0]</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> </span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> # write current FP to file</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="p">@@ -821,7 +821,7 @@</span> def extendReadDic(readdic):</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> """</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> internalnaming = 0</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> reverseReadDic = np.zeros(len(readdic), dtype='S50')</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for id in readdic.iterkeys():</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for id in readdic.keys():</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> # i</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> readdic[id] = ReadID(internalnaming, readdic[id])</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> reverseReadDic[internalnaming] = id</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="p">@@ -867,8 +867,8 @@</span> def CreateCompareList(Reference, ARG):</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> </span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="352" 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">
352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> if (len(reference) != len(artificialreference)):</span>
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<td class="diff-line-num new new_line" data-linenumber="353" 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">
353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "first 10 letter:\t\t" + reference[0:10] + "..." + reference[-10:]</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "last 10 letter:\t\t" + artificialreference[0:10] + "..." + artificialreference[-10:]</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("first 10 letter:\t\t" + reference[0:10] + "..." + reference[-10:])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="356" 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">
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("last 10 letter:\t\t" + artificialreference[0:10] + "..." + artificialreference[-10:])</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> print ("Error! Two Sequences have different length! Try to add a line break after the last nucleotide.")</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> sys.exit(1)</span>
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<td class="diff-line-num new new_line" data-linenumber="359" 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">
359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> else:</span>
</pre>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="p">@@ -921,7 +921,7 @@</span> def readSAMline(alignment, identifier, c</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> except:</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> gaps = 0</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> mism = 0</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 "Error Reading MDtag of %s.Setting gaps = 0,mism = 0" % readname</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Error Reading MDtag of %s.Setting gaps = 0,mism = 0" % readname)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> try:</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> nm = int(getNumberOf(tags, "NM"))</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> except:</span>
</pre>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="p">@@ -993,7 +993,7 @@</span> def ReadArtificialSAMfileHTSeq(art, comp</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> for alignment in fobj:</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> k += 1</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> if k % 1000000 == 0:</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("%d.." %(k/1000000)),</span></span>
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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(("%d.." %(k/1000000)), end=' ')</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> read, readname = isSaneAlignment(alignment, "art", compareList, readdic)</span>
</pre>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> if read == 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="377" 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">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> pass</span>
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<td class="diff-line-num new new_line" data-linenumber="378" 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">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="p">@@ -1019,7 +1019,7 @@</span> def ReadArtificialSAMfileHTSeq(art, comp</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"> fobj.close()</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> end = time.time()</span>
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<td class="diff-line-num new new_line" data-linenumber="381" 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">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> #print("\r\n")</span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("\t %f " % (end - start)),</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("\t %f " % (end - start)), end=' ')</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> #print ("\tdone in %d seconds" % (end-start))</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> return(artdic)</span>
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<td class="diff-line-num new new_line" data-linenumber="386" 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">
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="p">@@ -1039,7 +1039,7 @@</span> def writeToTabArt(ReadDic, outfile):</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> """</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> </span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> fobj = open(outfile, "a")</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for read in ReadDic.keys():</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;">+ for read in list(ReadDic.keys()):</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> BestReadIndex = np.array(ReadDic[read].nm).argmin()</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> fobj.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\r\n" % (read, ReadDic[read].mr[BestReadIndex], ReadDic[read].subs[BestReadIndex], ReadDic[read].nm[BestReadIndex], ReadDic[read].rq, ReadDic[read].mq[BestReadIndex], ReadDic[read].start[BestReadIndex], ReadDic[read].end[BestReadIndex], ReadDic[read].gaps[BestReadIndex], ReadDic[read].mism[BestReadIndex]))</span>
</pre>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> fobj.close()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="p">@@ -1065,7 +1065,7 @@</span> def writeToTabRef(RefArray, outfile, rev</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> """</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="398" 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">
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"> fobj = open(outfile, "a")</span>
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<td class="diff-line-num new new_line" data-linenumber="400" 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">
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;">- for i in xrange(0, len(RefArray)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="401" 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">
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;">+ for i in range(0, len(RefArray)):</span></span>
</pre>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> read = RefArray[i]</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> # check if entry == 0</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> if read == 0:</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/core/FindOrfs.py</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/FindOrfs.py</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</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;">+#!/usr/bin/python3</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> </span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> </span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> """</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> def build_ORF(sequence,file_ORF,pdic):</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"> START,STOP,STARTrev,STOPrev = find_orfs(sequence,pdic)</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> t=open(file_ORF,'a')</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 "\t search forward orfs..."</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("\t search forward orfs...")</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> orf_counter = 0</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> orf_name = "forw"</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> for i in START:</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span> def build_ORF(sequence,file_ORF,pdic):</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> </span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> orf_counter = 0</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> orf_name = "rev"</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t search backward orfs..."</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t search backward orfs...")</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> for i in STARTrev:</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> for j in STOPrev:</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> #3 conditions</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="p">@@ -66,7 +66,7 @@</span> def build_ORF(sequence,file_ORF,pdic):</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> t.write('\n')</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> pdic[i]="E"</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> pdic[j]="S"</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(str(temp+orf_counter))</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((str(temp+orf_counter)))</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> t.close()</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> </span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> return (pdic)</span>
</pre>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="p">@@ -207,10 +207,10 @@</span> def find_orfs(genomeSequence,pdic):</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> else:</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> break</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> ###test##################</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("START codons : " + str(len(start)))</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("STOP codons : " +str(len(stop)))</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("revSTART codons : " +str(len(startRev)))</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("revSTOP codons : " +str(len(stopRev)))</span></span>
</pre>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("START codons : " + str(len(start))))</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("STOP codons : " +str(len(stop))))</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("revSTART codons : " +str(len(startRev))))</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("revSTOP codons : " +str(len(stopRev))))</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> # FORWARD</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/core/InsertMutations.py</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/InsertMutations.py</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" 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="LC460" class="line" lang="diff"> """</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> Created 2012</span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> core Script for the generation of the artificial reference genome</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="p">@@ -16,7 +16,7 @@</span> unbalanced mutations, but this will caus</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> import random as r</span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import Prep as INI</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import Prep as INI</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span> def getMutation(AA,Codon):</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> temp_mutationlist = []</span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> '''create a list of possible triplets within hamming distance 1 '''</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for item in INI.genetic_code.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for item in list(INI.genetic_code.keys()):</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> isvalid = INI.isvalidtriplet(item,Codon)</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> ''' Hamming distance 1, AA is not equal to the given AA,forbid mutation to stopcodon '''</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> if (isvalid == True and AA !=INI.genetic_code[item] and INI.genetic_code[item]!="*"):</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="p">@@ -280,9 +280,9 @@</span> def mutate_random(DNA,AminoAcid,distance</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> </span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> # stats (INI.savepickle(pdic,header+"_pdic_e"))</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> print("\r\n########Some stats:########")</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("DNA length:\t" + str(len(DNA)))</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("max substitutions:\t" + str(len(DNA)/distance))</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("#Balanced Mutations:\t" + str(succ_counter))</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("DNA length:\t" + str(len(DNA))))</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("max substitutions:\t" + str(len(DNA)/distance)))</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("#Balanced Mutations:\t" + str(succ_counter)))</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> </span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> </span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> return ("".join(dna_list))</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/core/PlotData.py</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/PlotData.py</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="p">@@ -29,7 +29,7 @@</span> import pylab as p</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> </span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> def trapezoidal_rule(x, y):</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> """Approximates the integral through the points a,b"""</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- index = [i+1 for i in xrange(len(x)-1)]</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ index = [i+1 for i in range(len(x)-1)]</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> xdiff = np.array([x[i]-x[i-1] for i in index])</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> ysum = np.array([y[i]+y[i-1] for i in index])</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> return(np.dot(xdiff,ysum)/2)</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="p">@@ -105,7 +105,7 @@</span> def CalculateRoc2(dataArray,prefix,reads</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> </span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> tempids = [m.id for m in temparray]</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> uniquereads = {}</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0,len(tempids)):</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0,len(tempids)):</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> uniquereads[tempids[i]] = ""</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> </span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> mappedreads = len(uniquereads)</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="p">@@ -191,7 +191,7 @@</span> def CalculateRoc2(dataArray,prefix,reads</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> </span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> fobj = open(prefix+"_roctable.txt","w")</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> fobj.write("RQ\tGAPS\tMM\tPTP\tFP\tP\tSn\t1-Sp\tF\r\n")</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0,len(rocvector),1):</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0,len(rocvector),1):</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> temp = [str(k) for k in rocvector[i]]</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> tempstr = "\t".join(temp)</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> fobj.write(tempstr+"\r\n")</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/core/Prep.py</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/Prep.py</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span> Contains various help functions which in</span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> @author: Sven Giese'''</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle as pickle</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle as pickle</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> import random</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> ''' INIT DICTIONARIES '''</span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="p">@@ -145,7 +145,7 @@</span> def savepickle(dictionary,outputname):</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> """</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> pickle.dump( dictionary, open(outputname +".p", "wb" ) )</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Saved .pickle to: " + outputname +".p")</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Saved .pickle to: " + outputname +".p"))</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> def loadpickle(inputname):</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="p">@@ -158,5 +158,5 @@</span> def loadpickle(inputname):</span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> @return: Dictionary containing start and end positions of ORFs.</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> dictionary= pickle.load( open(inputname ))#+".p" ) )</span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Loaded "+inputname+" pickle!")</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Loaded "+inputname+" pickle!"))</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> return (dictionary)</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/core/ReadAndWrite.py</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/core/ReadAndWrite.py</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> '''</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"> Created 2012</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> </span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="p">@@ -61,12 +61,12 @@</span> def writeoverview(Ndic_G,aadic_G,Ndic_AR</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> </span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> sum1 =0</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> sum2= 0</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for item in Ndic_G.keys():</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for item in list(Ndic_G.keys()):</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> fobj.write(item +"\t"+str(Ndic_G[item])+"\t"+str(Ndic_AR[item])+"\t"+str(Ndic_G[item]-Ndic_AR[item])+"\n")</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> sum1 +=abs(Ndic_G[item]-Ndic_AR[item])</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> fobj.write(str(sum1)+"\n")</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> </span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for item in aadic_G.keys():</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for item in list(aadic_G.keys()):</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> fobj.write(item +"\t"+str(aadic_G[item])+"\t"+str(aadic_AR[item])+"\t"+str(aadic_G[item]-aadic_AR[item])+"\n")</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> sum2 +=abs(aadic_G[item]-aadic_AR[item])</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> fobj.write(str(sum2)+"\n")</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="p">@@ -93,13 +93,13 @@</span> def nucleotide_dist_seq(seq,txt_file,sha</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> </span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"> if (shallwrite==1):</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> output_file=open(txt_file,'w')</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for item in Nndic.keys():</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for item in list(Nndic.keys()):</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> Nndic[item]=Nndic[item]/float(s)</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> output_file.write(item + "\t" + str(Nndic[item])+"\n")</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> </span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> output_file.close()</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> else:</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for item in Nndic.keys():</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for item in list(Nndic.keys()):</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> Nndic[item]=Nndic[item]/float(s)</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> return (Nndic) #N can be used for checking: should be the same number in real</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"> # and artificial chromosome</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="p">@@ -129,13 +129,13 @@</span> def aa_dist_seq(seq,txt_file,shallwrite)</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> n=1</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> if (shallwrite==1):</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> output_file=open(txt_file,'w')</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for item in aadic.keys():</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for item in list(aadic.keys()):</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> aadic[item]=aadic[item]/float(n)</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> output_file.write(item + "\t" + str(aadic[item])+"\n")</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> </span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> output_file.close()</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> else:</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for item in aadic.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for item in list(aadic.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"> aadic[item]=aadic[item]/float(n)</span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"> return (aadic) </span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="p">@@ -183,6 +183,6 @@</span> def gethammingdistance(original,artifici</span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"> </span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> else:</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> not_hamming+=1</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("#hamming distance REF-ART\t"+ str(hamming))</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("avg. distance:\t" + str(len(original)/float(hamming)))</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("#hamming distance REF-ART\t"+ str(hamming)))</span></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("avg. distance:\t" + str(len(original)/float(hamming))))</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> print("###########################\r\n")</span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/core.AnalyseMapping-pysrc.html</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/core.AnalyseMapping-pysrc.html</span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> </table></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"> <h1 class="epydoc">Source Code for <a href="core.AnalyseMapping-module.html">Module core.AnalyseMapping</a></h1></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> <pre class="py-src"></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt></span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/python3</tt> </tt></span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">""" This script is used to evalulate the mapping results """</tt> </tt></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">HTSeq</tt> </tt></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/core.FindOrfs-pysrc.html</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> <h1 class="epydoc">Source Code for <a href="core.FindOrfs-module.html">Module core.FindOrfs</a></h1></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/python3</tt>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line">
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line">
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">"""
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/core.InsertMutations-pysrc.html</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/core.InsertMutations-pysrc.html</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> <h1 class="epydoc">Source Code for <a href="core.InsertMutations-module.html">Module core.InsertMutations</a></h1></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">"""
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">Created 2012
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">core Script for the generation of the artificial reference genome
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/core.ReadAndWrite-pysrc.html</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> <h1 class="epydoc">Source Code for <a href="core.ReadAndWrite-module.html">Module core.ReadAndWrite</a></h1></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> <pre class="py-src"></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt>
</tt></span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/python3</tt>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">'''
</tt> </tt></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">Created 2012
</tt> </tt></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">
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<a href="https://salsa.debian.org/med-team/arden/compare/8d01d92569c89adbe2002dd069df55a944d28c09...a57e711a89edf2e9d77524c8551959a575a7e0bd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">spelling.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2to3_new.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/arden/compare/8d01d92569c89adbe2002dd069df55a944d28c09...a57e711a89edf2e9d77524c8551959a575a7e0bd#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,4 +3,4 @@</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"># DH_VERBOSE := 1</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"></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">%:</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span></span></pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span></span></pre>
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