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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/36d77e12861ac04e070fbcb0894b9cde8c5c14ad">36d77e12</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-06T20:06:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.25+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/d2a6e3d7e3e36b41763270da49bb6d2c54a3e25f">d2a6e3d7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-06T20:06:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/365fcaad5e69299e809e3760f2da05b7d34d00bb">365fcaad</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-06T20:06:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/6.0.25+dfsg'
Update to upstream version '6.0.25+dfsg'
with Debian dir 35a0498a5133ff1de89c72cfdc9a8b41be5e82ad</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/dfbafe93f87f6d91ac91e280c60a88c3d41eeb91">dfbafe93</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-06T20:06:15+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/625ddb2a8fe50a736115943ed43db4138aa3a386">625ddb2a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-06T20:06:31+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
</a>
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<li class="file-stats">
<a href="#ff6936350384213d6f693f4d604134188ce088c8">
CHANGEUID
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">
proteinortho6.pl
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</li>
<li class="file-stats">
<a href="#3439148ea7017354388f7c55043cc84986c1c394">
src/proteinortho_grab_proteins.pl
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</ul>
<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9...625ddb2a8fe50a736115943ed43db4138aa3a386#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="273" 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">@@ -273,3 +273,6 @@</td>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="plaintext"> refined the Makefile for proteinortho_clustering, now it additionally tests if the program is executable with the -test option </span>
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<td class="diff-line-num old_line" data-linenumber="274" 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="diff-line-num new_line" data-linenumber="274" 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="LC274" class="line" lang="plaintext"> 12. Oct (5122)</span>
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<td class="diff-line-num new_line" data-linenumber="275" 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="LC275" class="line" lang="plaintext"> enhancement of the Makefile (more verbose, added standard compiler flags, cleanup)</span>
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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="276" style="width: 35px; color: rgba(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="LC276" class="line" lang="plaintext"> 2. Dez (5195)</span>
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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="277" style="width: 35px; color: rgba(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="LC277" class="line" lang="plaintext"> fixing proteinortho_grab_protein.pl (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/41)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(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="278" style="width: 35px; color: rgba(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="LC278" class="line" lang="plaintext"> and ids that are not found are printed to STDERR </span></pre>
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<li id="ff6936350384213d6f693f4d604134188ce088c8">
<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9...625ddb2a8fe50a736115943ed43db4138aa3a386#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">51<span class="idiff left right">22</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">51<span class="idiff left right">95</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9...625ddb2a8fe50a736115943ed43db4138aa3a386#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.25+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sun, 06 Dec 2020 20:06:31 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">proteinortho (6.0.24+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Fix baseline violation</span>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9...625ddb2a8fe50a736115943ed43db4138aa3a386#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> liblapack-dev | libatlas-base-dev | liblapack.so,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> diamond-aligner,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> procps</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/proteinortho</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://gitlab.com/paulklemm_PHD/proteinortho</span>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9...625ddb2a8fe50a736115943ed43db4138aa3a386#c9e37a96ac72f9ef076d7a41a57470524d63b36e"><strong>proteinortho6.pl</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">@@ -464,7 +464,7 @@ use POSIX;</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.2<span class="idiff left right">4</span></span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.2<span class="idiff left right">5</span></span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1 -> don't / be verbose</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1 -> don't / show debug data</span></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9...625ddb2a8fe50a736115943ed43db4138aa3a386#3439148ea7017354388f7c55043cc84986c1c394"><strong>src/proteinortho_grab_proteins.pl</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">@@ -28,8 +28,8 @@</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @author Paul Klemm</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @email klemmp@staff.uni-marburg.de</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @company Bioinformatics, University of Leipzig</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date 3<span class="idiff left right">0-04</span>-2020</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date 3<span class="idiff left right">-12</span>-2020</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,36 +144,54 @@ if($fail){</td>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">qdata</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># my $qdata_count = {};</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$numOfFastas</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$line_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="perl"><span class="k" style="font-weight: 600;"><span class="idiff left">unless</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$FH</span></span><span class="p"><span class="idiff">,'</span></span><span class="s1" style="color: #d14;"><span class="idiff"><</span></span><span class="p"><span class="idiff">',</span></span><span class="nv" style="color: #008080;"><span class="idiff">$query</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$<span class="idiff left">query</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">-</span></span><span class="p"><span class="idiff right">"){</span></span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="perl"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">foreach</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$line</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="bp" style="color: #999;"><span class="idiff">STDIN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="perl"><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="perl"><span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff">$line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=~</span></span><span class="sr" style="color: #009926;"><span class="idiff right">s/[\r\n]+$//</span></span><span class="p">;</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl"><span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$v</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$v</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">scalar</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">@ARGV_copy</span></span><span class="idiff"> </span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$v</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff right">)</span>{</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$<span class="idiff left">ARGV_copyiddone</span></span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">$v</span></span><span class="p"><span class="idiff">]){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">next</span></span><span class="p"><span class="idiff right">;}</span></span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="perl"> <span class="nv" style="color: #008080;"><span class="idiff left">$numOfFastas</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff right">;</span></span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="perl"><span class="p"><span class="idiff left right">}</span></span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="perl"><span class="k" style="font-weight: 600;"><span class="idiff left">our</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">@filenames</span></span><span class="p">;</span></span>
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155
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<td class="diff-line-num new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="perl"></span>
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156
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<td class="diff-line-num new_line old" data-linenumber="158" 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="LC156" class="line" lang="perl"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$line</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$line</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="p"><span class="idiff">""){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">next</span></span><span class="p"><span class="idiff right">;}</span></span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="perl"><span class="k" style="font-weight: 600;"><span class="idiff left">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$foundHeader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>
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157
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<td class="diff-line-num new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="perl"></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@sp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$line</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="nv" style="color: #008080;">@filenames</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@sp</span><span class="p">;</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@sp</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">3</span><span class="p">){</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@sp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@spp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># print STDERR (scalar keys %qdata)." vs ".($numOfFastas);</span></span>
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164
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="perl"></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$vv</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$vv</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$vv</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">processLine</span><span class="p">{</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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166
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="perl"></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^\(//</span><span class="p">;</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\)$//</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"> <span class="nv" style="color: #008080;">$line</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span> </span>
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169
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="perl"></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="perl"> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{"</span><span class="s2" style="color: #d14;">STDIN</span><span class="p">"}{</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]}</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">STDIN.OrthoGroup</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="p">;</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="perl"> <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="perl"> <span class="p">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@sp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$line</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="nv" style="color: #008080;">$foundHeader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@filenames</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@sp</span><span class="p">;</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@sp</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">3</span><span class="p">){</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@sp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@spp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]);</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="perl"></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="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$vv</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$vv</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$vv</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^\(//</span><span class="p">;</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\)$//</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="perl"> <span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">""</span></span>
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173
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="perl"> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$prefix</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.OrthoGroup</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="p">;</span></span>
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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
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="perl"> <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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174
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="perl"> <span class="p">}</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="perl"> <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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176
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="perl"> <span class="p">}</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="perl"> <span class="p">}</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="perl"> <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="perl"><span class="k" style="font-weight: 600;">unless</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH</span><span class="p">,'</span><span class="s1" style="color: #d14;"><</span><span class="p">',</span><span class="nv" style="color: #008080;">$query</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">-</span><span class="p">"){</span></span>
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<td class="diff-line-num new old_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">
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<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
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$line</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="bp" style="color: #999;">STDIN</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span> <span class="p">{</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$line</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">STDIN</span><span class="p">")</span> <span class="p">}</span></span>
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177
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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178
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@sp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="nv" style="color: #008080;">$del</span><span class="p">,</span><span class="nv" style="color: #008080;">$query</span><span class="p">);</span> </span>
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179
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@sp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" 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="211" 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">@@ -193,32 +211,17 @@ unless(open(my $FH,'<',$query)) {</td>
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193
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="perl"> <span class="nv" style="color: #008080;">$query_basename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span><span class="p">;</span></span>
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194
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="perl"> <span class="p">}</span></span>
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195
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="perl"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="perl"> <span class="nv" style="color: #008080;">@filenames</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="perl"> <span class="nv" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@sp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span><span class="nv" style="color: #008080;">$_</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="nv" style="color: #008080;">@filenames</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@sp</span><span class="p">;</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@sp</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">3</span><span class="p">){</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@sp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@spp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]);</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="perl"></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$vv</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$vv</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$vv</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^\(//</span><span class="p">;</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\)$//</span><span class="p">;</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="perl"></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="perl"> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query_basename</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.OrthoGroup</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="p">;</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="perl"> <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="perl"> <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="perl"> <span class="p">}</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">,</span> <span class="nv" style="color: #008080;">$query_basename</span><span class="p">)</span> <span class="p">}</span></span>
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218
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
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219
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] Done reading the query </span><span class="si" style="color: #d14;">$query</span><span class="s2" style="color: #d14;"> file. Now I know </span><span class="si" style="color: #d14;">$orthogroupcounter</span><span class="s2" style="color: #d14;"> groups with </span><span class="si" style="color: #d14;">$genecounter</span><span class="s2" style="color: #d14;"> genes/proteins in total.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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220
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="perl"><span class="p">}</span></span>
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221
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="perl"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="perl"></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$foundHeader</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$numOfFastas</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$genecounter</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">20</span><span class="p">){</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING : The header of the proteinortho file is missing, this can increase the runtime dramatically. Please include the first line (starting with '#'), to accelerate this program.</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="perl"><span class="p">}</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="perl"></span>
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$orthogroupcounter</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING : This call will produce </span><span class="si" style="color: #d14;">$orthogroupcounter</span><span class="s2" style="color: #d14;"> files (one for each orthology group) !</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">In the *.html file you can individually extract single groups by clicking on the front part of a row.</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$NC</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Press 'strg+c' to prevent me from proceeding or wait 20 seconds to continue...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -232,20 +235,16 @@ my $cur_gene_filename="";</td>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">cur_gene_firsttime</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$genecounterfound</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$numOfFastas</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV_copy</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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238
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copyiddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="perl"> <span class="nv" style="color: #008080;">$numOfFastas</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$fastai</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">foundIDs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV_copy</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copyiddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="perl"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$tofiles</span></span><span class="p"><span class="idiff">){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">[STDERR] (</span></span><span class="si" style="color: #d14;"><span class="idiff">$fastai</span></span><span class="s2" style="color: #d14;"><span class="idiff">/</span></span><span class="si" style="color: #d14;"><span class="idiff">$numOfFastas</span></span><span class="s2" style="color: #d14;"><span class="idiff">) : </span></span><span class="p"><span class="idiff">";</span></span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$basename</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">ne</span></span><span class="idiff"> </span><span class="p"><span class="idiff">""){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Done reading </span></span><span class="si" style="color: #d14;"><span class="idiff">$basename</span></span><span class="s2" style="color: #d14;"><span class="idiff">. </span></span><span class="p"><span class="idiff">"}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Start reading the fasta file </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$ARGV_copy</span></span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">$v</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff right">";}</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="perl"> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">[STDERR] (</span></span><span class="si" style="color: #d14;"><span class="idiff">$fastai</span></span><span class="s2" style="color: #d14;"><span class="idiff">/</span></span><span class="si" style="color: #d14;"><span class="idiff">$numOfFastas</span></span><span class="s2" style="color: #d14;"><span class="idiff">) : </span></span><span class="p"><span class="idiff">";</span></span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$basename</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">ne</span></span><span class="idiff"> </span><span class="p"><span class="idiff">""){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Done reading </span></span><span class="si" style="color: #d14;"><span class="idiff">$basename</span></span><span class="s2" style="color: #d14;"><span class="idiff">. </span></span><span class="p"><span class="idiff">"}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Start reading the fasta file </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$ARGV_copy</span></span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">$v</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff right">";</span></span></span>
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249
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="perl"> <span class="nv" style="color: #008080;">$fastai</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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250
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="perl"></span>
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251
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="perl"> <span class="nv" style="color: #008080;">$basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="297" 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="296" 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">@@ -297,6 +296,8 @@ for(my $v = 0 ; $v < scalar @ARGV_copy ; $v++){</td>
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<td class="diff-line-num old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
297
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="perl"> <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.fasta</span><span class="p">";</span></span>
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298
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="perl"> <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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299
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="perl"> <span class="nv" style="color: #008080;">$genecounterfound</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="perl"></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">};</span></span>
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300
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="perl"> <span class="p">}</span></span>
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301
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="302" 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">
302
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># fallback, if the basename (filename) does not exists, try all </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="305" 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="306" 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">@@ -305,20 +306,41 @@ for(my $v = 0 ; $v < scalar @ARGV_copy ; $v++){</td>
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305
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$geneprintswitch</span><span class="p">){</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>
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306
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<td class="diff-line-num new_line" data-linenumber="307" 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">
307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}})</span> <span class="p">{</span> </span>
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307
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$key</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$curLine_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
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308
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="perl"> </span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$doregex</span><span class="p">){</span><span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">quotemeta</span><span class="p">(</span><span class="nv" style="color: #008080;">$regexv</span><span class="p">);}</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="p">'</span><span class="s1" style="color: #d14;">\b</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;">\b</span><span class="p">';}</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$doregex</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">quotemeta</span><span class="p">(</span><span class="nv" style="color: #008080;">$regexv</span><span class="p">);}</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="perl"></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">){</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="perl"> </span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># use regular expression</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="perl"> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$curLine_test</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: #008080;">$regexv</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="perl"></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="perl"> </span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># directly compare starting with first 5 character of fasta entry as offset</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># start at 1 -> fasta entries starts with ">"</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">,</span><span class="nv" style="color: #008080;">$offset</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$key</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span> <span class="p">){</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"> <span class="nv" style="color: #008080;">$offset</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"> <span class="p">}</span> </span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"> <span class="p">}</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="perl"></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="p">){</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNI NG The input (</span><span class="si" style="color: #d14;">$key</span><span class="s2" style="color: #d14;">) was found multiple times in the fasta files </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">(maybe try --exact).</span><span class="p">"</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="p">")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="perl"> <span class="p">}</span></span>
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311
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="perl"></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: #008080;">$regexv</span> <span class="p">){</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="perl"> </span>
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314
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
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315
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$source</span><span class="p">){</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$basename</span><span class="p">;}</span></span>
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316
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="perl"></span>
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317
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="perl"> <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> </span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="perl"> <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;"><span class="idiff left right">=</span></span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.fasta</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="perl"> <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.fasta</span><span class="p">";</span></span>
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319
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="perl"> <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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320
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="perl"> <span class="nv" style="color: #008080;">$genecounterfound</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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321
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="perl"></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">};</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="perl"></span>
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322
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>
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323
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="perl"> <span class="p">}</span></span>
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324
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -352,6 +374,20 @@ if($genecounter != $genecounterfound){</td>
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352
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The input (</span><span class="si" style="color: #d14;">$query</span><span class="s2" style="color: #d14;">) contains </span><span class="si" style="color: #d14;">$genecounter</span><span class="s2" style="color: #d14;"> queries, but I extracted </span><span class="si" style="color: #d14;">$genecounterfound</span><span class="s2" style="color: #d14;"> entries out of the fasta(s).</span><span class="p">";</span></span>
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353
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<td class="diff-line-num new_line" data-linenumber="375" 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">
375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> If this is not desired, please consider using the -exact option</span><span class="p">";}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$genecounter</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$genecounterfound</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-> This should not have happen, maybe some fasta files are missing as input?</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">(If you cannot solve this error, please send a report to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com or visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for more help. Further more all mails to lechner</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">staff.uni-marburg.de are welcome)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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354
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="perl"></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="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$genecounterfound</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$genecounter</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The following ids were not found:</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$counter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></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="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$filename</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">qdata</span><span class="p">)</span> <span class="p">{</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}})</span> <span class="p">{</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span><span class="k" style="font-weight: 600;">last</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: #008080;">$key</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="perl"> <span class="p">}</span></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="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$counter</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="k" style="font-weight: 600;">last</span><span class="p">}</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please make sure that the upper ids are part of the given fasta files (try searching these in the given fasta files) !</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="perl"> <span class="p">}</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="perl"> </span>
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355
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="perl"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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356
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<td class="diff-line-num new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] All entries of the query are found in the fasta(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num old old_line" data-linenumber="357" 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">
357
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<td class="diff-line-num new_line old" data-linenumber="393" 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="LC357" class="line" lang="perl"><span class="p">}</span></span></pre>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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">\ No newline at end of file</td>
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<td class="diff-line-num new old_line" data-linenumber="358" style="width: 35px; color: rgba(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="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="perl"><span class="p">}</span></span></pre>
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