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<h3>
Steffen Möller pushed to branch upstream
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/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e">83071ae5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-12T23:17:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.12+dfsg</pre>
</li>
</ul>
<h4>9 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
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">
proteinortho6.pl
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<li class="file-stats">
<a href="#e88e2072d8bed1edd8ac79e979262281cfe9549b">
.gitlab-ci.yml
→
src/.gitlab-ci.yml
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<li class="file-stats">
<a href="#e52fa9f6246a270e3b0a6a888a797d22f02e2532">
src/proteinortho_ffadj_mcs.py
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<li class="file-stats">
<a href="#baed8b8088767318f56f01f49bec7ce10b85899f">
<span class="new-file">
+
src/proteinortho_history.pl
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<li class="file-stats">
<a href="#1486be463578edbd60b13d54cd9e0d2b9d4ecd99">
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+
src/proteinortho_summary.pl
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<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" 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="218" 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">@@ -218,9 +218,18 @@</td>
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext"> proteinortho6.pl replaced chomp with s/[\r\n]+$//</span>
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<td class="diff-line-num old_line" data-linenumber="219" 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="219" 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="LC219" class="line" lang="plaintext"> proteinortho_clustering.cpp fix bug that only uses lapack if -pld is set, regardless of the value.</span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"> 11. Sept (uid: 3813)</span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext"> updated shebang of ffadj such that python2.7 is used directly (ffadj fails if called with higher version of python)</span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="plaintext"> -p=blastp is now alias of blastp+ and legacy blast is now -p=blastp_legacy (blastn is equivalent)</span>
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<td class="diff-line-num old old_line" data-linenumber="223" 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="LC223" class="line" lang="plaintext"> Makefile: static now includes -lquadmath</span>
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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(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="LC221" class="line" lang="plaintext"> <span class="idiff left right"> </span>updated shebang of ffadj such that python2.7 is used directly (ffadj fails if called with higher version of python)</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> <span class="idiff left right"> </span>-p=blastp is now alias of blastp+ and legacy blast is now -p=blastp_legacy (blastn is equivalent)</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> <span class="idiff left right"> </span>Makefile: static now includes -lquadmath</span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="plaintext"> 25. Sept (uid: 3899)</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext"> synteny update to python3 (but the code looks fishy, the -synteny option now gets a deprecated warning)</span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="plaintext"> proteinortho now only print html for <10 files automatically and otherwise only gives the option</span></pre>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> synteny update to python3 (but the code looks fishy, the -synteny option now gets a deprecated warning)</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> proteinortho now only print html for <10 files automatically and otherwise only gives the option</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> 4. Nov (uid: 4020)</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> FIXED: sometimes the python3 version produces one edditional edge (global defintion of ALPHA). Special thanks for this update goes to Daniel Doerr for fixing this.</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> 25. Nov (uid: 4030)</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> added proteinortho_history</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> the synteny option ffadj is now not depricated anymore</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> 10. Dec (uid: 4196)</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> improved proteinortho_history</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> removed the new diamond spam</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> + added proteinortho_summary.pl for a summary of proteinortho-graph on species level.</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">3899</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">4196</span></span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="77" 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="77" 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">@@ -77,7 +77,7 @@ endif</td>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="make"><span class="nv" style="color: #008080;">dir_guard</span><span class="o" style="font-weight: 600;">=</span>@if <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Creating build directory ..."</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="make"></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">$(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_<span class="idiff left right">ffadj_mcs.py $(BUILDDIR)/proteinortho_clustering</span> $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_cleanupblastgraph $(BUILDDIR)/proteinortho_treeBuilderCore</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">$(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_<span class="idiff left right">summary.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_history.pl</span> $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_cleanupblastgraph $(BUILDDIR)/proteinortho_treeBuilderCore</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[100%] </span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">Everything is compiled with no errors.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="make"><span class="nl">$(BUILDDIR)/proteinortho_extract_from_graph.pl</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/proteinortho_extract_from_graph.pl</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" 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="120" 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">@@ -120,6 +120,14 @@ $(BUILDDIR)/proteinortho_ffadj_mcs.py: src/proteinortho_ffadj_mcs.py</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="make"> <span class="nv" style="color: #008080;">$(dir_guard)</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">cp</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="make"><span class="nl">$(BUILDDIR)/proteinortho_history.pl</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/proteinortho_history.pl</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="make"> <span class="nv" style="color: #008080;">$(dir_guard)</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">cp</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="make"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="make"><span class="nl">$(BUILDDIR)/proteinortho_summary.pl</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/proteinortho_summary.pl</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="make"> <span class="nv" style="color: #008080;">$(dir_guard)</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">cp</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$@</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="make"></span>
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123
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="make"><span class="nl">echoENV</span><span class="o" style="font-weight: 600;">:</span></span>
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124
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"CC = "</span></span>
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125
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$(CC)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" 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="232" 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">@@ -224,7 +232,7 @@ else</td>
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224
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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225
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="make"></span>
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226
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<td class="diff-line-num new_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">install</span></span>
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<td class="diff-line-num old old_line" data-linenumber="227" 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">
227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl proteinortho $(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho_<span class="idiff left right">cleanupblastgraph $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_treeBuilderCore $(BUILDDIR)/proteinortho_grab_proteins.pl</span></span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl proteinortho $(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho_<span class="idiff left right">history.pl $(BUILDDIR)/proteinortho_cleanupblastgraph $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_treeBuilderCore $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_summary.pl $(BUILDDIR)/proteinortho_history.pl </span></span></span>
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228
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"INSTALLING everything to </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">"</span></span>
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229
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-v</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="p">;</span></span>
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230
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<td class="diff-line-num new_line" data-linenumber="238" 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">
238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">Everything installed successfully to </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -246,15 +254,15 @@ test_step2: proteinortho6.pl</td>
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246
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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247
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="248" 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">
248
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<td class="diff-line-num new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="make"></span>
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<td class="diff-line-num old old_line" data-linenumber="249" 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">
249
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<td class="diff-line-num new_line old" data-linenumber="257" 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="LC249" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> @echo -n " [2/12] -p=blastp+ synteny (PoFF) test: "</span></span>
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<td class="diff-line-num old old_line" data-linenumber="250" 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">
250
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<td class="diff-line-num new_line old" data-linenumber="257" 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="LC250" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> @if [ "$(shell which blastp)" = "" ]; then\</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> echo "$(ORANGE)blastp missing, skipping...$(NC)"; \</span></span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> else \</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> ./proteinortho6.pl -silent -force -project=test_synteny -synteny -singles -p=blastp+ test/*.faa; \</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> set -e ; ./src/chk_test.pl test_synteny.proteinortho.tsv; \</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> set -e ; ./src/chk_test.pl test_synteny.poff.tsv; \</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> echo "$(GREEN)passed$(NC)"; \</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> fi</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="make"> <span class="nl">@echo -n " [2/12] -p=blastp+ synteny (PoFF) test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="s2" style="color: #d14;">which blastp</span><span class="nf" style="color: #900; font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">blastp missing, skipping...</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="make"> <span class="k" style="font-weight: 600;">else</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="make"> ./proteinortho6.pl <span class="nt" style="color: #000080;">-silent</span> <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_synteny <span class="nt" style="color: #000080;">-synteny</span> <span class="nt" style="color: #000080;">-singles</span> <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>blastp+ <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="make"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span> <span class="p">;</span> ./src/chk_test.pl test_synteny.proteinortho.tsv<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="make"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span> <span class="p">;</span> ./src/chk_test.pl test_synteny.poff.tsv<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>
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258
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<td class="diff-line-num new_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="make"></span>
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259
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<td class="diff-line-num new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="make"> <span class="nl">@echo -n " [3/12] -p=diamond test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">"</span></span>
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260
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<td class="diff-line-num new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="s2" style="color: #d14;">which diamond</span><span class="nf" style="color: #900; font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span><span class="se" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Proteinortho</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"> Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. Details can be found in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-124"</span><span class="nt" style="color: #000080;">></span>Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124.<span class="nt" style="color: #000080;"></a></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (doi:10.1371/journal.pone.0105015), is already build in Proteinortho. The general workflow of proteinortho is depicted <span class="p">[</span><span class="nv" style="color: #008080;">![here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.dropbox.com/s/7ubl1ginn3fmf8k/proteinortho_workflow.jpg?dl=0</span><span class="p">)</span>].</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">Proteinortho is a tool to detect orthologous genes within different species.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">Details can be found in (<span class="p">[</span><span class="nv" style="color: #008080;">doi:10.1186/1471-2105-12-124</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-124</span><span class="p">)</span>).</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (<span class="p">[</span><span class="nv" style="color: #008080;">doi:10.1371/journal.pone.0105015</span><span class="p">](</span><span class="sx" style="color: #d14;">https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105015</span><span class="p">)</span>), is already build in Proteinortho. The general workflow of proteinortho: </span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="gh" style="color: #999;"># New Features of Proteinortho Version 6!</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="nv" style="color: #008080;"><img src="https://www.uni-marburg.de/de/fb16/ipc/ag-lechner/graph.png/@@images/image/unimr_lead_image_sd" alt="proteinortho.workflow.png" height="250"></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">Input: multiple fasta files (orange box) with many proteins/genes (circles). </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">First an initial all vs. all comparison between all proteins of all species is performed to determine protein similarities (upper right image). </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">The second stage is the clustering of similar genes to meaningful co-orthologous groups (lower right image). Connected components within this graph can be considered as putative co-orthologous groups in theory and are returned in the output (lower left image).</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="gh" style="color: #999;"># New Features of Proteinortho Version 6</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p"> -</span> Implementation of various Blast alternatives for step (for -step=2 the -p= options): Diamond, MMseqs2, Last, Topaz, Rapsearch2, Blat, Ublast and Usearch</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p"> -</span> Multithreading support for the clustering step (-step=3)</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p"> -</span> Integration of the LAPACK Fortran Library for a faster clustering step (-step=3)</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p"> -</span> Integration of the bitscore weights in the connectivity calculation for more data dependant splits (-step=3)</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p"> -</span> Continuous Integration <span class="p">[</span><span class="nv" style="color: #008080;">![pipeline status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/badges/master/pipeline.svg</span><span class="p">)</span>](https://gitlab.com/paulklemm_PHD/proteinortho/pipelines) </span>
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12
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>
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13
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<td class="diff-line-num new_line old" data-linenumber="26" 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="LC13" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><summary></span>Minor features: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><summary></span>Minor <span class="idiff left right">new </span>features: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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14
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<td class="diff-line-num new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<td class="diff-line-num new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="p"> -</span> Output now supports OrthoXML (-xml) and HTML.</span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">proteinortho_history.pl</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs</span><span class="p">)</span> a new tool for tracking proteins (or pairs of proteins) in the workflow of proteinortho.</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">proteinortho_summary.pl</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs</span><span class="p">)</span></span>
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16
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<td class="diff-line-num new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="p"> -</span> Various test routines (make test).</span>
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17
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<td class="diff-line-num new_line" data-linenumber="32" 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">
32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p"> -</span> New heuristics for connectivity calculation (-step=3).</span>
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18
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="nt" style="color: #000080;"></details></span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><summary></span>6.0.12: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p"> -</span> removed the diamond spam</span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p"> -</span> improved <span class="p">[</span><span class="nv" style="color: #008080;">proteinortho_history.pl</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs</span><span class="p">)</span> : now the program is "smarter" in detecting files automatically</span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="p"> -</span> added <span class="p">[</span><span class="nv" style="color: #008080;">proteinortho_summary.pl</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs</span><span class="p">)</span> : a tool for summarizing the proteinortho-graph on species level. With the output it is easy to identify weak connected species. </span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="nt" style="color: #000080;"></details></span></span>
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19
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"><span class="gh" style="color: #999;"># Continuous Integration</span></span>
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21
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<td class="diff-line-num new_line old" data-linenumber="42" 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="LC21" class="line" lang="markdown">supports</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">The badge</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![pipeline status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/badges/master/pipeline.svg</span><span class="p">)</span>](https://gitlab.com/paulklemm_PHD/proteinortho/commits/master) indicates the current status of the continuous integration (CI) among various platforms (ubuntu, centos, debian, fedora) and GNU c++ versions (5, 6, latest)</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">The whole git repository gets deployed on a clean docker imager (gcc:latest,gcc:5,ubuntu:latest,fedora:latest,debian:latest,centos:latest) and compiled (make all) and tested (make test). The badge is green only if all test are passed. For more information see <span class="p">[</span><span class="nv" style="color: #008080;">Continuous Integration (proteinortho wiki)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Continuous%20Integration</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">A more detailed list of all changes: <span class="p">[</span><span class="nv" style="color: #008080;">CHANGELOG</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/blob/master/CHANGELOG</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="gh" style="color: #999;"># Table of Contents</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"><span class="p">1.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="48" 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">@@ -30,12 +48,18 @@ The whole git repository gets deployed on a clean docker imager (gcc:latest,gcc:</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="p">4.</span> <span class="p">[</span><span class="nv" style="color: #008080;">PoFF synteny extension</span><span class="p">](</span><span class="sx" style="color: #d14;">#poff</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="p">5.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Output description</span><span class="p">](</span><span class="sx" style="color: #d14;">#output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="p">6.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Examples</span><span class="p">](</span><span class="sx" style="color: #d14;">#examples</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="p">7.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Error Codes and Troubleshooting</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes</span><span class="p">)</span> <- look here if you cannot compile/run (proteinortho wiki)</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="p">8.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Large compute jobs example</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option</span><span class="p">)</span>) (proteinortho wiki)</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="p">9.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Biological example</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/biological-example</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">proteinortho</span> wiki)</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown">Bug reports: See chapter 7. or send a mail to incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com (Please include the 'Parameter-vector' that is printed for all errors)</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown">You can also send a mail to lechner@staff.uni-marburg.de.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="gh" style="color: #999;"># [Proteinortho-Wiki](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/) Table of Contents</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="p">1.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Tools and additional programs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">2.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Error Codes and Troubleshooting</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes</span><span class="p">)</span> <- look here if you cannot compile/run proteinortho</span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="p">3.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Large compute jobs example</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">4.</span> <span class="p">[</span><span class="nv" style="color: #008080;">FAQ</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/FAQ</span><span class="p">)</span> <span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">(...)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown">Bug reports: Please have a look at chapter <span class="p">[</span><span class="nv" style="color: #008080;">2.</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes</span><span class="p">)</span> first or send a mail to incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com. (please include the 'parameter-vector' that is printed for all errors)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown">You can also send mails to lechner@staff.uni-marburg.de. Any suggestions, feedback and comments are welcome!</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="gh" style="color: #999;"># Installation</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" 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="112" 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">@@ -88,7 +112,7 @@ Afterwards the deb package can be installed with `sudo dpkg -i proteinortho*deb`</td>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <span class="idiff left right">1. Prerequisites</span></span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <span class="idiff left right">Prerequisites for compiling proteinortho from source</span></span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown">Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></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">@@ -126,7 +150,7 @@ Proteinortho uses standard software which is often installed already or is part</td>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <span class="idiff left right">2. </span>Building and installing proteinortho from source (linux and osx)</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Building and installing proteinortho from source (linux and osx)</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"> Here you can use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.</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">@@ -179,7 +203,7 @@ OR(!) specify the new g++ in 'make CXX=/usr/local/bin/g++-7 all'</td>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">100%</span><span class="p">]</span> Everything is compiled with no errors.</span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="markdown"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="markdown">The compilation of proteinortho_clustering has multiple fall-back routines. If everything fails please look here <span class="p">[</span><span class="nv" style="color: #008080;">Troubleshooting (proteinortho wiki)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown">The compilation of proteinortho<span class="se" style="color: #d14;"><span class="idiff left right">\</span>_</span>clustering has multiple fall-back routines. If everything fails please look here <span class="p">[</span><span class="nv" style="color: #008080;">Troubleshooting (proteinortho wiki)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="markdown"><span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="markdown"></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">@@ -214,21 +238,13 @@ If you have problems compiling/running the program go to [Troubleshooting (prote</td>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="markdown"><span class="gh" style="color: #999;"># SYNOPSIS</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="markdown"><span class="gt" style="color: #a00;"> > **proteinortho6.pl [options] \<fasta file(s)\>** (one fasta for each species, at least 2)</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="markdown"> OR</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown"><span class="gt" style="color: #a00;"> > **proteinortho [options] \<fasta file(s)\>**</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"> one fasta for each species; at least 2</span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="markdown"><span class="gh" style="color: #999;"># DESCRIPTION</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**proteinortho**</span> is a tool to detect orthologous genes within different</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="markdown"> species. For doing so, it compares similarities of given gene sequences</span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="markdown"> and clusters them to find significant groups. The algorithm was designed</span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="markdown"> to handle large-scale data and can be applied to hundreds of species at</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="markdown"> one. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr</span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="markdown"> 28;12:124. To enhance the prediction accuracy, the relative order of genes</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="markdown"> (synteny) can be used as additional feature for the discrimination of</span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="markdown"> orthologs. The corresponding extension, namely PoFF (doi:10.1371/journal.pone.0105015), is already build in Proteinortho.</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"> species. </span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="markdown"> Proteinortho assumes, that you have all your gene sequences in FASTA</span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="markdown"> format either represented as amino acids or as nucleotides. The source</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="318" 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">@@ -302,6 +318,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="markdown"><span class="sb" style="color: #d14;"> - diamond : Only for protein files! standard diamond procedure and for</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="markdown"><span class="sb" style="color: #d14;"> genes/proteins of length >40 with the additional --sensitive flag</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Warning: Please use version 0.9.29 or later to avoid this known bug: https://gitlab.com/paulklemm_PHD/proteinortho/issues/24</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="markdown"><span class="sb" style="color: #d14;"> - lastn,lastp : lastal. -n : dna files, -p protein files (BLOSUM62</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="markdown"><span class="sb" style="color: #d14;"> scoring matrix)!</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="343" 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="360" 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">@@ -343,7 +360,6 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Synteny options (optional, step 2)**</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="markdown"> (This option is deprecated)</span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="markdown"> (output: <span class="nt" style="color: #000080;"><myproject></span>.ffadj-graph, <span class="nt" style="color: #000080;"><myproject></span>.poff.tsv (tab separated file)-graph)</span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></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">@@ -537,6 +553,9 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">myproject.proteinortho-graph.summary</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools-and-additional-programs#proteinortho-graphblast-graph-species-summary-table</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><summary></span> myproject.proteinortho.html (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="markdown"> The html version of the myproject.proteinortho.tsv file</span>
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<li id="c9e37a96ac72f9ef076d7a41a57470524d63b36e">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#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">@@ -341,8 +341,6 @@ By default, Proteinortho splits each group into two more dense subgroups when th</td>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 POFF (-synteny)</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">-->> This option is deprecated <<---</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The synteny based graph files (myproject.ffadj-graph and myproject.poff-graph) have two additional columns:</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">same_strand and simscore. The first one indicates if two genes from a match are located at the same strands (1) or not (-1).</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The second one is an internal score which can be interpreted as a normalized weight ranging from 0 to 1 based on the respective e-values.</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">@@ -455,7 +453,7 @@ use POSIX;</td>
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<pre style="margin: 0;"> <span id="LC453" 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="LC454" 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="LC455" 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="LC458" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.<span class="idiff left right">8</span></span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.<span class="idiff left right">12</span></span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>
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460
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<td class="diff-line-num new_line" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$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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<td class="diff-line-num old_line" data-linenumber="461" 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">
461
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459
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<pre style="margin: 0;"> <span id="LC459" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="595" 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="593" 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">@@ -595,9 +593,9 @@ foreach my $option (@ARGV) {</td>
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595
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?selfblast=(0|1)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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596
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?singles$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$singles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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597
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?singles=(0|1)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$singles</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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598
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<td class="diff-line-num new_line old" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?poff$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <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="si" style="color: #d14;"><span class="idiff">$ORANGE</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">[WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -->> This option is deprecated <<---</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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599
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<td class="diff-line-num new_line old" data-linenumber="596" 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="LC599" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</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="s2" style="color: #d14;"><span class="idiff">[WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -->> This option is deprecated <<---</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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600
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<td class="diff-line-num new_line old" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny=(0|1)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</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="s2" style="color: #d14;"><span class="idiff">[WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -->> This option is deprecated <<---</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?poff$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="idiff left"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#print STDERR "$ORANGE"."[WARNING]$NC -->> This option is deprecated <<---";</span></span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="idiff left"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#print STDERR "$ORANGE"."[WARNING]$NC -->> This option is deprecated <<---"; </span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny=(0|1)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p"><span class="idiff left">}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#print STDERR "$ORANGE"."[WARNING]$NC -->> This option is deprecated <<---"; </span></span></span>
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601
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<td class="diff-line-num new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?dups=0$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$duplication</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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602
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?dups=([1-8])$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$duplication</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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603
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?neighbourjoin$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$neighbourjoin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="606" 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="604" 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">@@ -606,9 +604,9 @@ foreach my $option (@ARGV) {</td>
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606
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?keep$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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607
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<td class="diff-line-num new_line" data-linenumber="605" 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">
605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?force$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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608
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?clean$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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609
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<td class="diff-line-num new_line old" data-linenumber="607" 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="LC609" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?help$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;"><span class="idiff left right">print_usag</span>e</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="610" style="width: 35px; color: rgba(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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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?help$/</span><span class="p">)</span> <span class="p">{</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="nv" style="color: #008080;"><span class="idiff">print_header</span></span><span class="p"><span class="idiff">;</span></span><span class="nv" style="color: #008080;"><span class="idiff right">print_usage_mor</span>e</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
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<td class="diff-line-num old_line" data-linenumber="610" 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">
610
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<td class="diff-line-num new_line" data-linenumber="608" 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">
608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?test$/</span><span class="p">)</span> <span class="p">{</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">check_bins</span><span class="p">;</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">get_po_path</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">All necessary proteinortho_* binaries are found.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?h$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?h$/</span><span class="p">)</span> <span class="p">{</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="nv" style="color: #008080;"><span class="idiff">print_header</span></span><span class="p"><span class="idiff right">;</span></span><span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
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612
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?nograph$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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613
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<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?xml$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$doxml</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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614
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?graph$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="622" 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="620" 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">@@ -622,6 +620,7 @@ foreach my $option (@ARGV) {</td>
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<td class="diff-line-num old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
622
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<td class="diff-line-num new_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span> <span class="p">"</span><span class="si" style="color: #d14;">$RED</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[Error]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Invalid command line option: </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">'</span><span class="si" style="color: #d14;">$option</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">'! </span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span> <span class="p">}</span></span>
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623
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621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="perl"><span class="p">}</span></span>
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624
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="perl"></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$jobnumber</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""</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="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> You should use the -tmp option in combination with -jobs.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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625
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$selfblast</span><span class="p">){</span><span class="nv" style="color: #008080;">$checkblast</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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626
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="perl"></span>
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627
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626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="perl"><span class="nv" style="color: #008080;">$po_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">get_po_path</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;"># Determine local path</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -856,7 +855,7 @@ sub cluster {</td>
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856
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
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857
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ci</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># first column = total</span></span>
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<td class="diff-line-num old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
858
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<td class="diff-line-num new_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="perl"> <span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.75</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
859
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<td class="diff-line-num new_line old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</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;">Clustering by similarity (Proteinortho mode) using </span><span class="si" style="color: #d14;"><span class="idiff left">$freemem_inMB</span></span><span class="s2" style="color: #d14;"><span class="idiff"> MB of memory (75% of total memory) and </span></span><span class="si" style="color: #d14;"><span class="idiff">$cpus</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> cpu core(s)</span>.</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="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Clustering by similarity (Proteinortho mode) using <span class="idiff left">up to </span></span><span class="si" style="color: #d14;"><span class="idiff">$freemem_inMB</span></span><span class="s2" style="color: #d14;"><span class="idiff"> MB of memory (75% of total memory) and </span></span><span class="si" style="color: #d14;"><span class="idiff">$cpus</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> cpu core(s). Adjust this behaviour with the -mem option</span>.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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860
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>
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861
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="perl"> <span class="p">}</span></span>
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862
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ci</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$ci</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="865" 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="864" 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">@@ -865,10 +864,10 @@ sub cluster {</td>
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865
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="perl"> <span class="p">}</span></span>
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866
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865
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<pre style="margin: 0;"> <span id="LC865" 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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<td class="diff-line-num old_line" data-linenumber="867" 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">
867
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<td class="diff-line-num new_line" data-linenumber="866" 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">
866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="perl"> <span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">16384</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="868" 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">
868
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<td class="diff-line-num new_line old" data-linenumber="867" 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="LC868" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Clustering by similarity (Proteinortho mode) using </span><span class="si" style="color: #d14;"><span class="idiff left">$freemem_inMB</span></span><span class="s2" style="color: #d14;"><span class="idiff"> MB of memory (default value, command 'free' not found) and </span></span><span class="si" style="color: #d14;"><span class="idiff">$cpus</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> cpu core(s)</span>.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</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;">Clustering by similarity (Proteinortho mode) using <span class="idiff left">up to </span></span><span class="si" style="color: #d14;"><span class="idiff">$freemem_inMB</span></span><span class="s2" style="color: #d14;"><span class="idiff"> MB of memory (default value, command 'free' not found) and </span></span><span class="si" style="color: #d14;"><span class="idiff">$cpus</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> cpu core(s). Adjust this behaviour with the -mem option</span>.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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869
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="perl"> <span class="p">}</span></span>
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870
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869
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<pre style="margin: 0;"> <span id="LC869" 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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871
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Clustering by similarity (Proteinortho mode) using </span><span class="si" style="color: #d14;"><span class="idiff left">$freemem_inMB</span></span><span class="s2" style="color: #d14;"><span class="idiff"> MB of memory and </span></span><span class="si" style="color: #d14;"><span class="idiff">$cpus</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> cpu core(s)</span>.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</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;">Clustering by similarity (Proteinortho mode) using <span class="idiff left">up to </span></span><span class="si" style="color: #d14;"><span class="idiff">$freemem_inMB</span></span><span class="s2" style="color: #d14;"><span class="idiff"> MB of memory and </span></span><span class="si" style="color: #d14;"><span class="idiff">$cpus</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> cpu core(s). Adjust this behaviour with the -mem option</span>.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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872
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="perl"> <span class="p">}</span></span>
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873
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#if($freemem_inMB < 5){if($verbose){print STDERR "$ORANGE"."[WARNING]$NC Increased the maximal memory threshold to 5 MB ($freemem_inMB MB is not sufficent).$NC\n";}$freemem_inMB=5;} # minimum 5 MB</span></span>
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874
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$freemem_inMB</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1000</span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The memory threshold of </span><span class="si" style="color: #d14;">$freemem_inMB</span><span class="s2" style="color: #d14;"> MB seems somewhat small. I will increase the threshold to 1 GB (-ram=1000).</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1024</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;"># minimum 5 MB</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -902,6 +901,7 @@ sub cluster {</td>
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902
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_singletons.pl </span><span class="si" style="color: #d14;">$fastas</span><span class="s2" style="color: #d14;"> <'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' >>'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>
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903
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="perl"> <span class="p">}</span></span>
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="perl"></span>
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905
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905
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<pre style="margin: 0;"> <span id="LC905" 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;">$nograph</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$useMcl</span><span class="p">)</span> <span class="p">{</span></span>
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906
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906
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_graphMinusRemovegraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' </span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">* >'</span><span class="si" style="color: #d14;">$csimgraph</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>
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907
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: #008080;">$keep</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: #008080;">$rm_simgraph</span><span class="p">);}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="909" 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="909" 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">@@ -909,6 +909,9 @@ sub cluster {</td>
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909
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$useMcl</span><span class="p">){</span></span>
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910
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</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;">[OUTPUT] -> Orthologous pairs are written to </span><span class="si" style="color: #d14;">$csimgraph</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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911
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="perl"> <span class="p">}</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">x</span> <span class="p">"</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_summary.pl</span><span class="p">"){</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_summary.pl '</span><span class="si" style="color: #d14;">$csimgraph</span><span class="s2" style="color: #d14;">' >>'</span><span class="si" style="color: #d14;">$csimgraph</span><span class="s2" style="color: #d14;">.summary'</span><span class="p">");</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="perl"> <span class="p">}</span></span>
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912
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915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="perl"></span>
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913
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<td class="diff-line-num new_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span><span class="p">){</span></span>
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914
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917
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">perl </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho2html.pl </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> ></span><span class="si" style="color: #d14;">$simtablehtml</span><span class="p">");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="951" 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="954" 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">@@ -951,7 +954,10 @@ sub cluster {</td>
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951
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<td class="diff-line-num new_line" data-linenumber="954" 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">
954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$useMcl</span><span class="p">){</span></span>
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<td class="diff-line-num old_line" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
952
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<td class="diff-line-num new_line" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</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;">[OUTPUT] -> Orthologous pairs are written to </span><span class="si" style="color: #d14;">$csyngraph</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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953
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="perl"> <span class="p">}</span></span>
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954
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<td class="diff-line-num new_line old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">x</span> <span class="p">"</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_summary.pl</span><span class="p">"){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_summary.pl '</span><span class="si" style="color: #d14;">$csyngraph</span><span class="s2" style="color: #d14;">' >>'</span><span class="si" style="color: #d14;">$csyngraph</span><span class="s2" style="color: #d14;">.summary'</span><span class="p">");</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="perl"> <span class="p">}</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="perl"> </span>
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955
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<td class="diff-line-num new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">perl </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho2html.pl </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> ></span><span class="si" style="color: #d14;">$syntablehtml</span><span class="p">");</span></span>
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<td class="diff-line-num old_line" data-linenumber="956" 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">
956
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<td class="diff-line-num new_line" data-linenumber="962" 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">
962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$syntablehtml</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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957
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="995" 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="1001" 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">@@ -995,21 +1001,83 @@ Options:</td>
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995
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="perl"></span>
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996
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<td class="diff-line-num new_line" data-linenumber="1002" 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">
1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Search options]</span></span>
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997
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<td class="diff-line-num new_line" data-linenumber="1003" 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">
1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="perl"><span class="s2" style="color: #d14;"> -p= blast program [default: diamond]</span></span>
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998
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<td class="diff-line-num new_line old" data-linenumber="1004" 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="LC998" class="line" lang="perl"><span class="s2" style="color: #d14;"> {blast*|tblastx|blast*+|tblastx+|diamond|usearch|ublast|lastp|lastn|rapsearch|topaz|*blat*|mmseqs*}</span></span>
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999
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="perl"><span class="s2" style="color: #d14;"> blast*|tblastx : standard blast family (blastp : protein files, blastn : dna files)</span></span>
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="perl"><span class="s2" style="color: #d14;"> blast*+|tblastx+ : standard blastal family (blastp+ : protein files, blastn+ : dna files)</span></span>
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1001
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="perl"><span class="s2" style="color: #d14;"> blast*_legacy : legacy blast family</span></span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="perl"><span class="s2" style="color: #d14;"> diamond : Only for protein files! standard diamond procedure and for genes/proteins of length >40 with the additional --sensitive flag</span></span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="perl"><span class="s2" style="color: #d14;"> usearch : usearch_local procedure with -id 0 (minimum identity percentage).</span></span>
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1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="perl"><span class="s2" style="color: #d14;"> ublast : usearch_ublast procedure.</span></span>
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1005
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="perl"><span class="s2" style="color: #d14;"> lastn : standard lastal. Only for dna files!</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="perl"><span class="s2" style="color: #d14;"> lastp : lastal using -p and BLOSUM62 scoring matrix. Only for protein files!</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="perl"><span class="s2" style="color: #d14;"> rapsearch : Only for protein files!</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="perl"><span class="s2" style="color: #d14;"> topaz : Only for protein files!</span></span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="perl"><span class="s2" style="color: #d14;"> blat* : Blat family. blatp : Only for protein files! blatn : Only for dna files! blatx : Only for dna files!</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="perl"><span class="s2" style="color: #d14;"> mmseqs* : mmseqs family. mmseqsp : Only for protein files! mmseqsn : Only for dna files! blatx : Only for dna files!</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="perl"><span class="s2" style="color: #d14;"> {blastp|blastn|tblastx|blastp_legacy|blastn_legacy|tblastx_legacy|diamond|usearch|ublast|lastp|lastn|rapsearch|topaz|blatp|blatn|mmseqsp|mmseqsn}</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="perl"><span class="s2" style="color: #d14;"> The suffix 'p' or 'n' indicates aminoacid fasta files (p) or nucleotide fasta files (n).</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="perl"><span class="s2" style="color: #d14;"> The suffix '_legacy' indicates legacy blastall (otherwise blast+ is used).</span></span>
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1011
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1007
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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="perl"><span class="s2" style="color: #d14;"> -e= E-value for blast [default: 1e-05]</span></span>
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1012
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="perl"></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Synteny options]</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="perl"><span class="s2" style="color: #d14;"> -synteny activate PoFF extension to separate similar sequences print</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="perl"><span class="s2" style="color: #d14;"> by contextual adjacencies (requires .gff for each .fasta)</span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="perl"><span class="s2" style="color: #d14;"> -alpha= PoFF: weight of adjacencies vs. sequence similarity</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="perl"><span class="s2" style="color: #d14;"> (default: 0.5)</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="perl"></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Clustering options]</span></span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="perl"><span class="s2" style="color: #d14;"> -singles report singleton genes without any hit</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="perl"><span class="s2" style="color: #d14;"> -conn= min. algebraic connectivity [default: 0.1]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="perl"><span class="s2" style="color: #d14;"> -xml produces an OrthoXML formatted file of the *.proteinortho.</span></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="perl"><span class="s2" style="color: #d14;"> (...) show more with --help</span></span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="perl"><span class="s2" style="color: #d14;">For more information see the man page: 'proteinortho -man' or online: https://gitlab.com/paulklemm_PHD/proteinortho</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="perl"><span class="s2" style="color: #d14;">Or you can use the GUI proteinorthoHelper.html (available at http://lechnerlab.de/proteinortho/)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="perl"><span class="s2" style="color: #d14;">Do you have suggestions or need more help: write a mail to lechner</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">@staff</span><span class="s2" style="color: #d14;">.uni-marburg.de.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="perl"><span class="p">";</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1013" style="width: 35px; color: rgba(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="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">print_usage_more</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1030
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<pre style="margin: 0;">+<span id="LC1030" 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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="perl"><span class="s2" style="color: #d14;"> |</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="perl"><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;"> /</span><span class="si" style="color: #d14;">${NC}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${RED2}</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$NC</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="perl"><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;"> /</span><span class="se" style="color: #d14;">\\</span><span class="si" style="color: #d14;">${NC}${RED2}</span><span class="s2" style="color: #d14;"> /</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$NC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="perl"><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;">/ </span><span class="si" style="color: #d14;">${RED2}</span><span class="s2" style="color: #d14;">/</span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${RED2}</span><span class="se" style="color: #d14;">\\</span><span class="si" style="color: #d14;">${NC}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="perl"><span class="s2" style="color: #d14;">Usage: proteinortho6.pl [OPTIONS] FASTA1 FASTA2 [FASTA...] (one for each species, at least 2)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="perl"><span class="s2" style="color: #d14;">Options:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="perl"><span class="s2" style="color: #d14;"> [General options]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="perl"><span class="s2" style="color: #d14;"> -project= prefix for all result file names [default: myproject]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="perl"><span class="s2" style="color: #d14;"> -cpus= number of processors to use [default: auto]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="perl"><span class="s2" style="color: #d14;"> -ram= maximal used ram threshold for LAPACK and the input graph in MB [default: 75% of the total memory]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="perl"><span class="s2" style="color: #d14;"> -silent sets verbose to 0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="perl"><span class="s2" style="color: #d14;"> -temp= path for temporary files [default: working directory]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="perl"><span class="s2" style="color: #d14;"> -keep stores temporary blast results for reuse</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="perl"><span class="s2" style="color: #d14;"> -force forces the recalculation of the blast results in any case in step=2. Also forces the recreation of the database generation in step=1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="perl"><span class="s2" style="color: #d14;"> -clean remove all unnecessary files after processing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step= 1 -> generate indices</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="perl"><span class="s2" style="color: #d14;"> 2 -> run blast (and ff-adj, if -synteny is set)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="perl"><span class="s2" style="color: #d14;"> 3 -> clustering</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="perl"><span class="s2" style="color: #d14;"> 0 -> all (default)</span></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="perl"></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Search options]</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="perl"><span class="s2" style="color: #d14;"> -p= blast program [default: diamond]</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="perl"><span class="s2" style="color: #d14;"> {blastp|blastn|tblastx|blastp_legacy|blastn_legacy|tblastx_legacy|diamond|usearch|ublast|lastp|lastn|rapsearch|topaz|blatp|blatn|mmseqsp|mmseqsn}</span></span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="perl"></span>
</pre>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="perl"><span class="s2" style="color: #d14;"> The program need to be installed first.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="perl"><span class="s2" style="color: #d14;"> A suffix 'p' or 'n' indicates aminoacid fasta files (p) or nucleotide fasta files (n).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="perl"><span class="s2" style="color: #d14;"> The '_legacy' suffix indicates legacy blastall (otherwise blast+ is used).</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="perl"></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="perl"><span class="s2" style="color: #d14;"> blast*|tblastx : standard blast+ family (blastp : protein files, blastn : dna files)</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="perl"><span class="s2" style="color: #d14;"> blast*_legacy : legacy blast family (blastall)</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="perl"><span class="s2" style="color: #d14;"> diamond : Only for protein files! standard diamond procedure and for genes/proteins of length >40 with the additional --sensitive flag</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="perl"><span class="s2" style="color: #d14;"> usearch : usearch_local procedure with -id 0 (minimum identity percentage).</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="perl"><span class="s2" style="color: #d14;"> ublast : usearch_ublast procedure.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="perl"><span class="s2" style="color: #d14;"> lastn : standard lastal. Only for dna files!</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="perl"><span class="s2" style="color: #d14;"> lastp : lastal using -p and BLOSUM62 scoring matrix. Only for protein files!</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="perl"><span class="s2" style="color: #d14;"> rapsearch : Only for protein files!</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="perl"><span class="s2" style="color: #d14;"> topaz : Only for protein files!</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="perl"><span class="s2" style="color: #d14;"> blat* : Blat family. blatp : For protein files! blatn : For dna files! blatx : For dna files!</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="perl"><span class="s2" style="color: #d14;"> mmseqs* : mmseqs family. mmseqsp : For protein files! mmseqsn : For dna files! blatx : For dna files!</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="perl"><span class="s2" style="color: #d14;"> -e= E-value for blast [default: 1e-05]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="perl"><span class="s2" style="color: #d14;"> -selfblast apply selfblast, detects paralogs without orthologs</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="perl"><span class="s2" style="color: #d14;"> -sim= min. similarity for additional hits (0..1) [default: 0.95]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="perl"><span class="s2" style="color: #d14;"> -identity= min. percent identity of best blast hits [default: 25]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="perl"><span class="s2" style="color: #d14;"> -cov= min. coverage of best blast alignments in % [default: 50]</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1013" style="width: 35px; color: rgba(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="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="perl"><span class="s2" style="color: #d14;"> -subpara= additional parameters for the search tool</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="perl"><span class="s2" style="color: #d14;"> example -subpara='-seg no' or -subpara='--more-sensitive' for diamond</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="perl"></span>
</pre>
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1013
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<td class="diff-line-num new_line" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Synteny options]</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1014" 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">
1014
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<td class="diff-line-num new_line" data-linenumber="1082" 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">
1082
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="perl"><span class="s2" style="color: #d14;"> -synteny activate PoFF extension to separate similar sequences print</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1015" 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">
1015
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<td class="diff-line-num new_line" data-linenumber="1083" 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">
1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="perl"><span class="s2" style="color: #d14;"> by contextual adjacencies (requires .gff for each .fasta)</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1023" 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="1091" 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">@@ -1023,16 +1091,36 @@ Options:</td>
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1023
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<td class="diff-line-num new_line" data-linenumber="1091" 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">
1091
</td>
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Clustering options]</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1024" 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">
1024
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<td class="diff-line-num new_line" data-linenumber="1092" 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">
1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="perl"><span class="s2" style="color: #d14;"> -singles report singleton genes without any hit</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1025" 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">
1025
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<td class="diff-line-num new_line" data-linenumber="1093" 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">
1093
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1093" class="line" lang="perl"><span class="s2" style="color: #d14;"> -conn= min. algebraic connectivity [default: 0.1]</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1026" 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">
1026
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="perl"><span class="s2" style="color: #d14;"> -xml produces an OrthoXML formatted file of the *.proteinortho.</span></span>
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1027
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="perl"></span>
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1028
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="perl"><span class="s2" style="color: #d14;"> (...)</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="perl"><span class="s2" style="color: #d14;"> -xml produces an OrthoXML formatted file of the *.proteinortho.tsv file.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="perl"><span class="s2" style="color: #d14;"> -purity= avoid spurious graph assignments, the higher the more uncertain edges are cut [0-1, default: 1e-07]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="perl"><span class="s2" style="color: #d14;"> -mcl enables the mcl algorithm for clustering instead of power iteration or lapacks routine. (needs mcl to be installed) </span></span>
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<td class="diff-line-num new new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="perl"><span class="s2" style="color: #d14;"> -nograph do not generate .proteinortho-graph file (pairwise orthology relations)</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Misc options]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="perl"><span class="s2" style="color: #d14;"> -desc write description files (for NCBI FASTA input only)</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="perl"><span class="s2" style="color: #d14;"> -debug gives detailed information for bug tracking</span></span>
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1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="perl"><span class="s2" style="color: #d14;"> -binpath= path to your directory of local programs that are not available globally (this should not be needed)</span></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="perl"><span class="s2" style="color: #d14;"> [Large compute jobs]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="perl"><span class="s2" style="color: #d14;"> In case jobs should be distributed onto several machines, use</span></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="perl"><span class="s2" style="color: #d14;"> -jobs=M/N N defines the number of defined job groups (e.g. PCs)</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="perl"><span class="s2" style="color: #d14;"> M defines the set of jobs to run in this process</span></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="perl"></span>
</pre>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="perl"><span class="s2" style="color: #d14;"> Example: run with </span></span>
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<td class="diff-line-num new new_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step=1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="perl"><span class="s2" style="color: #d14;"> to prepare data then to split a run on two machines use</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="perl"><span class="s2" style="color: #d14;"> -jobs=1/2 -step=2 on PC one and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="perl"><span class="s2" style="color: #d14;"> -jobs=2/2 -step=2 on PC two</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="perl"><span class="s2" style="color: #d14;"> finally run with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step=3 to finalize</span></span>
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1029
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="perl"></span>
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1030
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<td class="diff-line-num new_line" data-linenumber="1117" 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">
1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="perl"><span class="s2" style="color: #d14;">For more information see the man page: 'proteinortho -man' or online: https://gitlab.com/paulklemm_PHD/proteinortho</span></span>
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1031
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<td class="diff-line-num new_line" data-linenumber="1118" 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">
1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="perl"><span class="s2" style="color: #d14;">Or you can use the GUI proteinorthoHelper.html (available at http://lechnerlab.de/proteinortho/)</span></span>
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1032
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<td class="diff-line-num new_line old" data-linenumber="1119" 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="LC1032" class="line" lang="perl"><span class="s2" style="color: #d14;">Dou have suggestions or need more help: write a mail to lechner</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">@staff</span><span class="s2" style="color: #d14;">.uni-marburg.de.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="perl"><span class="s2" style="color: #d14;">Do<span class="idiff left right"> yo</span>u have suggestions or need more help: write a mail to lechner</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">@staff</span><span class="s2" style="color: #d14;">.uni-marburg.de.</span></span>
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1033
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="perl"></span>
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1034
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="perl"><span class="p">";</span></span>
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1035
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1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="perl"><span class="p">}</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="perl"></span>
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1036
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1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># -memory= the amount of ram used for partioning in MB [default 75% of the total memory]</span></span>
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1037
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1125
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="perl"></span>
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1038
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1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">init_graph_output</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1584" 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="1672" 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">@@ -1584,12 +1672,12 @@ sub get_legal_matches {</td>
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1584
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1672
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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="perl"></span>
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1585
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1673
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<pre style="margin: 0;"> <span id="LC1673" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># if(($blastmode ne "phmmer" && $blastmode ne "jackhmmer")){ #workaround for jackhmmer + phmmer</span></span>
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1586
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<td class="diff-line-num new_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1674
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<pre style="margin: 0;"> <span id="LC1674" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Percent identity</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1587
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<pre style="margin: 0;">-<span id="LC1587" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$twilight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$local_identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$identity</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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1588
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<pre style="margin: 0;">-<span id="LC1588" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$twilight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$local_identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">identitybylength</span><span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span><span class="p">))</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1675
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<pre style="margin: 0;">+<span id="LC1675" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$twilight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$local_identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$identity</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$debug</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">!</span></span><span class="si" style="color: #d14;"><span class="idiff">$query_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -> </span></span><span class="si" style="color: #d14;"><span class="idiff">$subject_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> is removed because of identity threshold</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1676
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<pre style="margin: 0;">+<span id="LC1676" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$twilight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$local_identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">identitybylength</span><span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span><span class="p">))</span> <span class="p">{</span><span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$debug</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">!</span></span><span class="si" style="color: #d14;"><span class="idiff">$query_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -> </span></span><span class="si" style="color: #d14;"><span class="idiff">$subject_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> is removed because of identity by length threshold</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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1589
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<td class="diff-line-num new_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1677
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<pre style="margin: 0;"> <span id="LC1677" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Min. length</span></span>
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1590
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1678
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<pre style="margin: 0;"> <span id="LC1678" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx+</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$alignment_length</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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<td class="diff-line-num old old_line" data-linenumber="1591" 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">
1591
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<td class="diff-line-num new_line old" data-linenumber="1679" 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="LC1591" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$length</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: #008080;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</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="1592" 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">
1592
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<td class="diff-line-num new_line old" data-linenumber="1679" 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="LC1592" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$length</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: #008080;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</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 old_line" data-linenumber="1593" style="width: 35px; color: rgba(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="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1679
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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$length</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: #008080;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$debug</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">!</span></span><span class="si" style="color: #d14;"><span class="idiff">$query_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -> </span></span><span class="si" style="color: #d14;"><span class="idiff">$subject_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> is removed because of coverage threshold</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1680
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<pre style="margin: 0;">+<span id="LC1680" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$length</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: #008080;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$debug</span></span><span class="p"><span class="idiff">)</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">!</span></span><span class="si" style="color: #d14;"><span class="idiff">$query_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -> </span></span><span class="si" style="color: #d14;"><span class="idiff">$subject_id</span></span><span class="s2" style="color: #d14;"><span class="idiff"> is removed because of coverage threshold</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";}</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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1593
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1681
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<pre style="margin: 0;"> <span id="LC1681" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1594" 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">
1594
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1682
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># It hit itself (only during selfblast)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1595" 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">
1595
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<td class="diff-line-num new_line" data-linenumber="1683" 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">
1683
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<pre style="margin: 0;"> <span id="LC1683" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if ($selfblast && $query_id eq $subject_id) {next;} # 5.16 reuse IDs</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1667,12 +1755,12 @@ sub generate_indices {</td>
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<td class="diff-line-num old_line" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1667
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<td class="diff-line-num new_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1755
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<pre style="margin: 0;"> <span id="LC1755" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</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;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1668
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<td class="diff-line-num new_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1756
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1669
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<td class="diff-line-num new_line" data-linenumber="1757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1757
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<pre style="margin: 0;"> <span id="LC1757" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</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;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1670
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<td class="diff-line-num new_line old" data-linenumber="1758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1670" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null<span class="idiff left"> 2></span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/null</span></span><span class="p">");</span></span>
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1671
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<td class="diff-line-num new_line" data-linenumber="1759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1759
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<pre style="margin: 0;"> <span id="LC1759" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</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;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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1672
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<td class="diff-line-num new_line" data-linenumber="1760" 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">
1760
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<pre style="margin: 0;"> <span id="LC1760" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1673" 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">
1673
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<td class="diff-line-num new_line" data-linenumber="1761" 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">
1761
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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">mkdir</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB</span><span class="p">");</span></span>
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<td class="diff-line-num old_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1674
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<td class="diff-line-num new_line" data-linenumber="1762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1762
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<pre style="margin: 0;"> <span id="LC1762" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</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;">$oldkeep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keep</span><span class="p">;</span><span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1675
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<td class="diff-line-num new_line old" data-linenumber="1763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1675" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</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 class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1676" style="width: 35px; color: rgba(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="1763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null<span class="idiff left"> 2></span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">/dev</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/null</span></span><span class="p">");</span></span>
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<td class="diff-line-num old_line" data-linenumber="1676" 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">
1676
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<td class="diff-line-num new_line" data-linenumber="1764" 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">
1764
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<pre style="margin: 0;"> <span id="LC1764" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1677" 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">
1677
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<td class="diff-line-num new_line" data-linenumber="1765" 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">
1765
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<pre style="margin: 0;"> <span id="LC1765" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</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;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this failes too, then there is something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">@incoming</span><span class="s2" style="color: #d14;">.gitlab.com.</span><span class="p">");}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1678" 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">
1678
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<td class="diff-line-num new_line" data-linenumber="1766" 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">
1766
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<pre style="margin: 0;"> <span id="LC1766" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1901" 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="1989" 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">@@ -1901,7 +1989,6 @@ sub blast {</td>
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<td class="diff-line-num old_line" data-linenumber="1901" 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">
1901
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<td class="diff-line-num new_line" data-linenumber="1989" 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">
1989
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<pre style="margin: 0;"> <span id="LC1989" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">This should not happen! Please submit the FASTA file(s) and the parameter vector (above) to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">@incoming</span><span class="s2" style="color: #d14;">.gitlab.com to help fixing this issue.</span><span class="p">");}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1902" 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">
1902
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<td class="diff-line-num new_line" data-linenumber="1990" 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">
1990
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<pre style="margin: 0;"> <span id="LC1990" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">##MARK_FOR_NEW_BLAST_ALGORITHM</span></span>
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<td class="diff-line-num old_line" data-linenumber="1903" 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">
1903
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<td class="diff-line-num new_line" data-linenumber="1991" 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">
1991
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<pre style="margin: 0;"> <span id="LC1991" class="line" lang="perl"></span>
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<td class="diff-line-num old old_line" data-linenumber="1904" 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">
1904
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<td class="diff-line-num new_line old" data-linenumber="1992" 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="LC1904" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1905" 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">
1905
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<td class="diff-line-num new_line" data-linenumber="1992" 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">
1992
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<pre style="margin: 0;"> <span id="LC1992" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># File does not exists yet or I am forced to rewrite it</span></span>
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<td class="diff-line-num old_line" data-linenumber="1906" 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">
1906
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<td class="diff-line-num new_line" data-linenumber="1993" 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">
1993
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<pre style="margin: 0;"> <span id="LC1993" 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="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$bla</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$force</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1907" 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">
1907
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<td class="diff-line-num new_line" data-linenumber="1994" 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">
1994
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<pre style="margin: 0;"> <span id="LC1994" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1909" 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="1996" 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">@@ -1909,7 +1996,7 @@ sub blast {</td>
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<td class="diff-line-num old_line" data-linenumber="1909" 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">
1909
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<td class="diff-line-num new_line" data-linenumber="1996" 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">
1996
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<pre style="margin: 0;"> <span id="LC1996" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1910" 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">
1910
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<td class="diff-line-num new_line" data-linenumber="1997" 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">
1997
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<pre style="margin: 0;"> <span id="LC1997" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</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="si" style="color: #d14;">$command</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># 5.16</span></span>
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<td class="diff-line-num old_line" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1911
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<td class="diff-line-num new_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1998
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<pre style="margin: 0;"> <span id="LC1998" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">diamond</span><span class="p">")</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1912" 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">
1912
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<td class="diff-line-num new_line old" data-linenumber="1999" 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="LC1912" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$command2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">diamond view --threads </span><span class="si" style="color: #d14;">$threads_per_process</span><span class="s2" style="color: #d14;"> --quiet -a </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.daa -o </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">";</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1999
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<pre style="margin: 0;">+<span id="LC1999" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$command2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">diamond view --threads </span><span class="si" style="color: #d14;">$threads_per_process</span><span class="s2" style="color: #d14;"> --quiet -a </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.daa -o </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp<span class="idiff left"> >/dev/null </span></span><span class="si" style="color: #d14;"><span class="idiff right">$printSTDERR</span></span><span class="p">";</span></span>
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<td class="diff-line-num old_line" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1913
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<td class="diff-line-num new_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="s2" style="color: #d14;"> && </span><span class="si" style="color: #d14;">$command2</span><span class="p">");</span> <span class="c1" style="color: #998; font-style: italic;"># run diamond and presort</span></span>
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<td class="diff-line-num old_line" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1914
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<td class="diff-line-num new_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2001
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<pre style="margin: 0;"> <span id="LC2001" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1915" 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">
1915
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<td class="diff-line-num new_line" data-linenumber="2002" 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">
2002
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<pre style="margin: 0;"> <span id="LC2002" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most likely errorsources of this are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2170" 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="2257" 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">@@ -2170,13 +2257,18 @@ sub check_bins {</td>
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2170
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<td class="diff-line-num new_line" data-linenumber="2257" 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">
2257
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<pre style="margin: 0;"> <span id="LC2257" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Please call -p=mmseqsp for protein datasets and -p=mmseqsn for nucleotide datasets.</span><span class="p">");</span></span>
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<td class="diff-line-num old_line" data-linenumber="2171" 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">
2171
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<td class="diff-line-num new_line" data-linenumber="2258" 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">
2258
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<pre style="margin: 0;"> <span id="LC2258" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2172" 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">
2172
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<td class="diff-line-num new_line" data-linenumber="2259" 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">
2259
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<pre style="margin: 0;"> <span id="LC2259" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">diamond</span><span class="p">")</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2173
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<td class="diff-line-num new_line old" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2173" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">diamond version</span><span class="p">";</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2260
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<pre style="margin: 0;">+<span id="LC2260" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">diamond version<span class="idiff left right"> 2>/dev/null</span></span><span class="p">";</span></span>
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<td class="diff-line-num old_line" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2174
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<td class="diff-line-num new_line" data-linenumber="2261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2261
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<pre style="margin: 0;"> <span id="LC2261" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qx($cmd 2>&1)</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2175
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<td class="diff-line-num new_line" data-linenumber="2262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2262
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<pre style="margin: 0;"> <span id="LC2262" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$out</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$out</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/diamond\sversion\s(.+)\n/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2176" 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">
2176
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<td class="diff-line-num new_line" data-linenumber="2263" 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">
2263
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<pre style="margin: 0;"> <span id="LC2263" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@version</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;">/\s+/</span><span class="p">,</span><span class="nv" style="color: #008080;">$1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2177
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<td class="diff-line-num new_line" data-linenumber="2264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2264
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<pre style="margin: 0;"> <span id="LC2264" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@version</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2178" 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">
2178
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<td class="diff-line-num new_line" data-linenumber="2265" 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">
2265
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<pre style="margin: 0;"> <span id="LC2265" class="line" lang="perl"> <span class="nv" style="color: #008080;">$makedb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">diamond makedb --in</span><span class="p">";</span></span>
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<td class="diff-line-num old_line" data-linenumber="2179" 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">
2179
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<td class="diff-line-num new_line" data-linenumber="2266" 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">
2266
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<pre style="margin: 0;"> <span id="LC2266" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2267
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<pre style="margin: 0;">+<span id="LC2267" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$versionnumber</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^0\.9\.(\d+)/</span><span class="p">){</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">29</span><span class="p">){</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2268
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<pre style="margin: 0;">+<span id="LC2268" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!! </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' version </span><span class="si" style="color: #d14;">$versionnumber</span><span class="s2" style="color: #d14;"> has a known bug that incorrectly computes the length of an alignment, thus the coverage threshold can produce wrong results leading in false negatives. See https://gitlab.com/paulklemm_PHD/proteinortho/issues/24 for more details.</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;"> >>> Please update diamond to 0.9.29 or higher <<<</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2180" style="width: 35px; color: rgba(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="2269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2269
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<pre style="margin: 0;">+<span id="LC2269" 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;">Press 'strg+c' to prevent me from proceeding or wait 10 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="diff-line-num new old_line" data-linenumber="2180" style="width: 35px; color: rgba(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="2270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2270
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<pre style="margin: 0;">+<span id="LC2270" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2180" style="width: 35px; color: rgba(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="2271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2271
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<pre style="margin: 0;">+<span id="LC2271" 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;">Well then, proceeding...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";}</span> <span class="p">}</span></span>
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2180
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<td class="diff-line-num new_line" data-linenumber="2272" 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">
2272
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<pre style="margin: 0;"> <span id="LC2272" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2181" 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">
2181
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<td class="diff-line-num new_line" data-linenumber="2273" 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">
2273
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<pre style="margin: 0;"> <span id="LC2273" 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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<td class="diff-line-num old_line" data-linenumber="2182" 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">
2182
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<td class="diff-line-num new_line" data-linenumber="2274" 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">
2274
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<pre style="margin: 0;"> <span id="LC2274" 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="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Failed to detect '</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">'.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please install </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;"> (or specify another binpath with -binpath=/home/...)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">I try now -p=blastp+ as fallback.</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2474,29 +2566,29 @@ sub get_po_path {</td>
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2474
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2566
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<pre style="margin: 0;"> <span id="LC2566" class="line" lang="perl"> <span class="nv" style="color: #008080;">$uname</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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<td class="diff-line-num old_line" data-linenumber="2475" 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">
2475
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<td class="diff-line-num new_line" data-linenumber="2567" 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">
2567
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<pre style="margin: 0;"> <span id="LC2567" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2476" 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">
2476
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<td class="diff-line-num new_line" data-linenumber="2568" 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">
2568
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<pre style="margin: 0;"> <span id="LC2568" 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;">x</span> <span class="p">"</span><span class="s2" style="color: #d14;">proteinortho_clustering</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2477" 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">
2477
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<td class="diff-line-num new_line old" data-linenumber="2569" 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="LC2477" class="line" lang="perl"> <span class="nv" style="color: #008080;"><span class="idiff left">$tmppath</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</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 right">""</span>;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2478" 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">
2478
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<td class="diff-line-num new_line old" data-linenumber="2569" 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="LC2478" 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">$debug</span></span><span class="p"><span class="idiff">){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Detected </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$tmppath</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</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 old old_line" data-linenumber="2479" 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">
2479
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<td class="diff-line-num new_line old" data-linenumber="2569" 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="LC2479" class="line" lang="perl"> <span class="p"><span class="idiff left">}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">elsif</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$tmppath</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">/src/proteinortho_clustering</span></span><span class="p"><span class="idiff right">"){</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="2480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2480
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<td class="diff-line-num new_line old" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2480" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$<span class="idiff left">tmppath</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">/src</span></span><span class="p"><span class="idiff right">"</span>;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2481
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<td class="diff-line-num new_line old" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2481" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</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;">Detected </span><span class="p"><span class="idiff left">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$tmppath</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff right">"</span></span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2569
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<pre style="margin: 0;">+<span id="LC2569" class="line" lang="perl"> <span class="k" style="font-weight: 600;"><span class="idiff left">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">`</span></span><span class="sb" style="color: #d14;"><span class="idiff">whereis proteinortho_clustering</span></span><span class="p"><span class="idiff right">`</span>;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2482" style="width: 35px; color: rgba(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="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2570
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<pre style="margin: 0;">+<span id="LC2570" class="line" lang="perl"> <span class="nv" style="color: #008080;"><span class="idiff left">$p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=~</span></span><span class="sr" style="color: #009926;"><span class="idiff">s/^proteinortho_clustering: *([^ ]+)\/proteinortho_clustering.*$/$1/</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2571
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<pre style="margin: 0;">+<span id="LC2571" class="line" lang="perl"> <span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">chomp</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$p</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2482" style="width: 35px; color: rgba(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="2572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2572
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<pre style="margin: 0;">+<span id="LC2572" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$<span class="idiff left right">p</span></span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2482" style="width: 35px; color: rgba(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="2573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2573
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<pre style="margin: 0;">+<span id="LC2573" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</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;">Detected <span class="idiff left right">(PATH enviroment variable)</span></span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2482" 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">
2482
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<td class="diff-line-num new_line" data-linenumber="2574" 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">
2574
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<pre style="margin: 0;"> <span id="LC2574" 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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<td class="diff-line-num old_line" data-linenumber="2483" 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">
2483
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<td class="diff-line-num new_line" data-linenumber="2575" 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">
2575
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<pre style="margin: 0;"> <span id="LC2575" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">/proteinortho_clustering</span><span class="p">"){</span></span>
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<td class="diff-line-num old_line" data-linenumber="2484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2484
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<td class="diff-line-num new_line" data-linenumber="2576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2576
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<pre style="margin: 0;"> <span id="LC2576" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="p">";</span></span>
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<td class="diff-line-num old_line" data-linenumber="2485" 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">
2485
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<td class="diff-line-num new_line" data-linenumber="2577" 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">
2577
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<pre style="margin: 0;"> <span id="LC2577" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span 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 old_line" data-linenumber="2486" 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">
2486
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<td class="diff-line-num new_line" data-linenumber="2578" 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">
2578
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2578" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">x</span> <span class="p">"</span><span class="s2" style="color: #d14;">/usr/bin/proteinortho_clustering</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2487" 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">
2487
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<td class="diff-line-num new_line old" data-linenumber="2579" 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="LC2487" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">/usr/bin</span><span class="p">";</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2579
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<pre style="margin: 0;">+<span id="LC2579" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">/usr/bin<span class="idiff left right">/</span></span><span class="p">";</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2488" 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">
2488
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<td class="diff-line-num new_line" data-linenumber="2580" 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">
2580
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<pre style="margin: 0;"> <span id="LC2580" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span 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 old_line" data-linenumber="2489" 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">
2489
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<td class="diff-line-num new_line" data-linenumber="2581" 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">
2581
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2581" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">x</span> <span class="p">"</span><span class="s2" style="color: #d14;">/usr/local/bin/proteinortho_clustering</span><span class="p">"){</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2490" 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">
2490
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<td class="diff-line-num new_line old" data-linenumber="2582" 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="LC2490" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">/usr/local/bin</span><span class="p">";</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2582
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<pre style="margin: 0;">+<span id="LC2582" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">/usr/local/bin<span class="idiff left right">/</span></span><span class="p">";</span></span>
</pre>
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2491
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<td class="diff-line-num new_line" data-linenumber="2583" 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">
2583
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<pre style="margin: 0;"> <span id="LC2583" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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2492
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<td class="diff-line-num new_line" data-linenumber="2584" 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">
2584
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<pre style="margin: 0;"> <span id="LC2584" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">x</span> <span class="p">"</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">/proteinortho_clustering</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2493
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<td class="diff-line-num new_line old" data-linenumber="2585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2493" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$binpath</span><span class="p">";</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2585
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<pre style="margin: 0;">+<span id="LC2585" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;"><span class="idiff left right">/</span></span><span class="p">";</span></span>
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<td class="diff-line-num old_line" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2494
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<td class="diff-line-num new_line" data-linenumber="2586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2586
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2586" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</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;">Detected </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span 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 old_line" data-linenumber="2495" 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">
2495
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<td class="diff-line-num new_line" data-linenumber="2587" 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">
2587
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2587" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2496" 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">
2496
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<td class="diff-line-num new_line" data-linenumber="2588" 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">
2588
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<pre style="margin: 0;"> <span id="LC2588" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2497" 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">
2497
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<td class="diff-line-num new_line" data-linenumber="2589" 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">
2589
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2589" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2498" 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">
2498
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<td class="diff-line-num new_line" data-linenumber="2590" 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">
2590
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<pre style="margin: 0;"> <span id="LC2590" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_clustering</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2499" 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">
2499
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<td class="diff-line-num new_line old" data-linenumber="2591" 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="LC2499" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_clustering in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;"> , /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2500" style="width: 35px; color: rgba(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="2591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2591
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<pre style="margin: 0;">+<span id="LC2591" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_clustering in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;"> , /usr/bin, /usr/local/bin, </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">\</span></span><span class="si" style="color: #d14;"><span class="idiff">$PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">, </span>-binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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2500
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<td class="diff-line-num new_line" data-linenumber="2592" 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">
2592
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<pre style="margin: 0;"> <span id="LC2592" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2501" 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">
2501
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<td class="diff-line-num new_line" data-linenumber="2593" 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">
2593
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<pre style="margin: 0;"> <span id="LC2593" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2502" 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">
2502
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<td class="diff-line-num new_line" data-linenumber="2594" 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">
2594
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<pre style="margin: 0;"> <span id="LC2594" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if(!-x "$tmppath[1]/proteinortho_cleanupblastgraph"){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2508" 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="2600" 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">@@ -2508,7 +2600,7 @@ sub get_po_path {</td>
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<td class="diff-line-num old_line" data-linenumber="2508" 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">
2508
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<td class="diff-line-num new_line" data-linenumber="2600" 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">
2600
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<pre style="margin: 0;"> <span id="LC2600" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># exit 0;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2509" 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">
2509
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<td class="diff-line-num new_line" data-linenumber="2601" 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">
2601
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2601" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># }</span></span>
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<td class="diff-line-num old_line" data-linenumber="2510" 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">
2510
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<td class="diff-line-num new_line" data-linenumber="2602" 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">
2602
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<pre style="margin: 0;"> <span id="LC2602" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho2html.pl</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2511
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<td class="diff-line-num new_line old" data-linenumber="2603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2511" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho2html.pl in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2603
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<pre style="margin: 0;">+<span id="LC2603" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho2html.pl in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">\</span></span><span class="si" style="color: #d14;"><span class="idiff">$PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">, </span>-binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2512" 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">
2512
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<td class="diff-line-num new_line" data-linenumber="2604" 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">
2604
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<pre style="margin: 0;"> <span id="LC2604" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2513" 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">
2513
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<td class="diff-line-num new_line" data-linenumber="2605" 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">
2605
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2605" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2514" 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">
2514
</td>
<td class="diff-line-num new_line" data-linenumber="2606" 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">
2606
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2606" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if(!-x "$tmppath[1]/proteinortho2tree.pl"){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2516" 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="2608" 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">@@ -2516,23 +2608,23 @@ sub get_po_path {</td>
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<td class="diff-line-num old_line" data-linenumber="2516" 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">
2516
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<td class="diff-line-num new_line" data-linenumber="2608" 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">
2608
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<pre style="margin: 0;"> <span id="LC2608" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># exit 0;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2517" 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">
2517
</td>
<td class="diff-line-num new_line" data-linenumber="2609" 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">
2609
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2609" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># }</span></span>
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<td class="diff-line-num old_line" data-linenumber="2518" 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">
2518
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<td class="diff-line-num new_line" data-linenumber="2610" 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">
2610
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2610" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_ffadj_mcs.py</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$synteny</span><span class="p">){</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2519
</td>
<td class="diff-line-num new_line old" data-linenumber="2611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2519" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_ffadj_mcs.py</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2520" style="width: 35px; color: rgba(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="2611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2611
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2611" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_ffadj_mcs.py</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">\</span></span><span class="si" style="color: #d14;"><span class="idiff">$PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">, </span>-binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2520" 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">
2520
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<td class="diff-line-num new_line" data-linenumber="2612" 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">
2612
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2612" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2521" 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">
2521
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<td class="diff-line-num new_line" data-linenumber="2613" 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">
2613
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2613" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2522" 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">
2522
</td>
<td class="diff-line-num new_line" data-linenumber="2614" 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">
2614
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2614" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_singletons.pl</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2523
</td>
<td class="diff-line-num new_line old" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC2523" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_singletons.pl</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2524" style="width: 35px; color: rgba(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="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2615
</td>
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<pre style="margin: 0;">+<span id="LC2615" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_singletons.pl</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">\</span></span><span class="si" style="color: #d14;"><span class="idiff">$PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">, </span>-binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2524" 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">
2524
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<td class="diff-line-num new_line" data-linenumber="2616" 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">
2616
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<pre style="margin: 0;"> <span id="LC2616" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2525" 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">
2525
</td>
<td class="diff-line-num new_line" data-linenumber="2617" 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">
2617
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2617" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2526" 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">
2526
</td>
<td class="diff-line-num new_line" data-linenumber="2618" 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">
2618
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2618" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_graphMinusRemovegraph</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2527
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<td class="diff-line-num new_line old" data-linenumber="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2527" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_graphMinusRemovegraph</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2528" style="width: 35px; color: rgba(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="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2619
</td>
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<pre style="margin: 0;">+<span id="LC2619" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_graphMinusRemovegraph</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">\</span></span><span class="si" style="color: #d14;"><span class="idiff">$PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">, </span>-binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2528" 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">
2528
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<td class="diff-line-num new_line" data-linenumber="2620" 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">
2620
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2620" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2529" 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">
2529
</td>
<td class="diff-line-num new_line" data-linenumber="2621" 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">
2621
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<pre style="margin: 0;"> <span id="LC2621" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2530" 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">
2530
</td>
<td class="diff-line-num new_line" data-linenumber="2622" 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">
2622
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2622" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_do_mcl.pl</span><span class="p">"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2531
</td>
<td class="diff-line-num new_line old" data-linenumber="2623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2531" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_do_mcl.pl</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2623
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2623" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_do_mcl.pl</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">\</span></span><span class="si" style="color: #d14;"><span class="idiff">$PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">, </span>-binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2532" 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">
2532
</td>
<td class="diff-line-num new_line" data-linenumber="2624" 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">
2624
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2624" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2533" 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">
2533
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<td class="diff-line-num new_line" data-linenumber="2625" 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">
2625
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2625" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2534" 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">
2534
</td>
<td class="diff-line-num new_line" data-linenumber="2626" 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">
2626
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2626" 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;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho2xml.pl</span><span class="p">"){</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2535
</td>
<td class="diff-line-num new_line old" data-linenumber="2627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2535" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho2xml.pl</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
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<pre style="margin: 0;">+<span id="LC2627" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho2xml.pl</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">\</span></span><span class="si" style="color: #d14;"><span class="idiff">$PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">, </span>-binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<pre style="margin: 0;"> <span id="LC2628" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2629
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<pre style="margin: 0;"> <span id="LC2629" class="line" lang="perl"> <span class="p">}</span></span>
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2630
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<pre style="margin: 0;"> <span id="LC2630" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#e88e2072d8bed1edd8ac79e979262281cfe9549b"><strong>.gitlab-ci.yml</strong>
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<strong>src/.gitlab-ci.yml</strong>
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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">@@ -2,7 +2,7 @@ variables:</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"> <span class="na" style="color: #008080;">PROJECT_NAME</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Proteinortho"</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "starting yml for Proteinortho"</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get update && apt-get -y install cmake diffutils wget ncbi-blast+ time git</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get update && apt-get -y install cmake diffutils wget ncbi-blast+ time git<span class="idiff left right"> python3</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">stages</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">codequality</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">test-precompiled-bins</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">@@ -17,7 +17,7 @@ gcc-latest-alloptions:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir ~/bin</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond ~/bin</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">perl proteinortho*pl -project=testasd -cpus=1 -ram=100 -verbose=2 -selfblast -silent -force -desc -checkfasta -cleanblast -debug -binpath=~/bin -tmp='~/' -e=0.000001 -sim=0.9 -identity=20 -cov=30 -subparaBlast='--more-sensitive' -synteny -dups=1 -cs=4 -alpha=0.4 -conn=0.01 -purity=0.00001 -minspecies=2 -subparaCluster='-cpus 1 -seed 1' -nograph -singles -xml -exactstep3 test/*faa >/dev/null 2>&1 && rm testasd*poff* && rm testasd*fadj* && rm testasd*info* && export LC_NUMERIC="C" && export LC_ALL="C" && for f in testasd.*; do sort $f >$f.testasd; done; sha256sum -b *testasd | tr -d '\n' | awk '{if($0 == "eb88ba29afd4f2dba16d3dbf97a5b0d2ab7686654a854f8502f0e778628e7f56 *testasd.descriptions.testasdf80df4c1a951bfb55b02300a273f6395694f01e8ae908e296d9c14a847d432ac *testasd.proteinortho.html.testasdfa18e9a0530f5a5754f045cfe97deaf818bdb5eb725619952633f1da0641cf7b *testasd.proteinortho.tsv.testasdc598b8c43e48e06614ec19e2f6b870e2737a7117a50ab2b1613880764d0884b2 *testasd.proteinortho.tsv.xml.testasd"){print $0." -> OK"; exit 0}else{print $0." -> failed"; exit 1}}'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">perl proteinortho*pl -project=testasd -cpus=1 -ram=100 -verbose=2 -selfblast -silent -force -desc -checkfasta -cleanblast -debug -binpath=~/bin -tmp='~/' -e=0.000001 -sim=0.9 -identity=20 -cov=30 -subparaBlast='--more-sensitive' -synteny -dups=1 -cs=4 -alpha=0.4 -conn=0.01 -purity=0.00001 -minspecies=2 -subparaCluster='-cpus 1 -seed 1' -nograph -singles -xml -exactstep3 test/*faa >/dev/null 2>&1 && rm testasd*poff* && rm testasd*fadj* && rm testasd*info* && export LC_NUMERIC="C" && export LC_ALL="C" && for f in testasd.*; do sort $f >$f.testasd; done; sha256sum -b *testasd | tr -d '\n' | awk '{if($0 == "eb88ba29afd4f2dba16d3dbf97a5b0d2ab7686654a854f8502f0e778628e7f56 *testasd.descriptions.testasd<span class="idiff left right">e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 *testasd.proteinortho-graph.summary.testasd</span>f80df4c1a951bfb55b02300a273f6395694f01e8ae908e296d9c14a847d432ac *testasd.proteinortho.html.testasdfa18e9a0530f5a5754f045cfe97deaf818bdb5eb725619952633f1da0641cf7b *testasd.proteinortho.tsv.testasdc598b8c43e48e06614ec19e2f6b870e2737a7117a50ab2b1613880764d0884b2 *testasd.proteinortho.tsv.xml.testasd"){print $0." -> OK"; exit 0}else{print $0." -> failed"; exit 1}}'</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"><span class="na" style="color: #008080;">gcc-latest-all-p</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</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">@@ -96,7 +96,7 @@ ubuntu-latest0:</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">test-precompiled-bins</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y update && apt-get -y install gcc && apt-get -y install gfortran && apt-get -y install build-essential g++</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y update && apt-get -y install gcc && apt-get -y install gfortran && apt-get -y install build-essential g++<span class="idiff left right"> && apt-get -y install python3</span></span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing topaz"</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/ajm/topaz</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd topaz/src</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,7 +115,7 @@ ubuntu-latest:</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">recompile-and-test</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y update && apt-get -y install gcc && apt-get -y install gfortran && apt-get -y install build-essential g++</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y update && apt-get -y install gcc && apt-get -y install gfortran && apt-get -y install build-essential g++<span class="idiff left right"> && apt-get -y install python3</span></span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing topaz"</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/ajm/topaz</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd topaz/src</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,7 +136,7 @@ debian-latest:</td>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">debian</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">recompile-and-test</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y update && apt-get -y install gcc && apt-get -y install gfortran && apt-get -y install build-essential g++</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">apt-get -y update && apt-get -y install gcc && apt-get -y install gfortran && apt-get -y install build-essential g++<span class="idiff left right"> && apt-get -y install python3</span></span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing topaz"</span></span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/ajm/topaz</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd topaz/src</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">@@ -153,34 +153,33 @@ debian-latest:</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make all</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make test</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="yaml"><span class="na" style="color: #008080;">fedora-latest</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">fedora</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="yaml"> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">test-precompiled-bins</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y groupinstall "Development Tools"</span> </span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install gcc-c++</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install cmake</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install make</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install tar</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install which</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install wget</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install libstdc++-static</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install lapack-static</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install cpan</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install python</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install ncbi-blast+</span></span>
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<td class="diff-line-num old old_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cpan Thread::Queue</span></span>
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<td class="diff-line-num old old_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tar -xzvf ncbi-blast*-x64-linux.tar.gz</span></span>
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<td class="diff-line-num old old_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cp ncbi-blast*/bin/blastp $HOME</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cp ncbi-blast*/bin/makeblastdb $HOME</span></span>
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<td class="diff-line-num old old_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing diamond"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="178" 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">
178
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<td class="diff-line-num new_line old" data-linenumber="156" 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="LC178" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond $HOME</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$PATH:$HOME"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" 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">
182
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<td class="diff-line-num new_line old" data-linenumber="156" 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="LC182" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "start proteinortho tests"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" 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">
183
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<td class="diff-line-num new_line old" data-linenumber="156" 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="LC183" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make test</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#fedora-latest:</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># image: fedora</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># stage: test-precompiled-bins</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># script:</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y groupinstall "Development Tools" </span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install gcc-c++</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install cmake</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install make</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install tar</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install which</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install wget</span></span>
</pre>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install libstdc++-static</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install lapack-static</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install cpan</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - yum -y install ncbi-blast+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - cpan Thread::Queue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - tar -xzvf ncbi-blast*-x64-linux.tar.gz</span></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="yaml"><span class="c1" style="color: #998; font-style: italic;"># - cp ncbi-blast*/bin/blastp $HOME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - cp ncbi-blast*/bin/makeblastdb $HOME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - echo "installing diamond"</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="yaml"><span class="c1" style="color: #998; font-style: italic;"># - wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz</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="yaml"><span class="c1" style="color: #998; font-style: italic;"># - tar xzf diamond-linux64.tar.gz</span></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="yaml"><span class="c1" style="color: #998; font-style: italic;"># - cp diamond $HOME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - export PATH="$PATH:$HOME"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># - echo "start proteinortho tests"</span></span>
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184
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<td class="diff-line-num new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="yaml"></span>
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<td class="diff-line-num old_line" data-linenumber="185" 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">
185
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<td class="diff-line-num new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="yaml"><span class="na" style="color: #008080;">centos-latest</span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="186" 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">
186
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<td class="diff-line-num new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">centos</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="192" 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">@@ -193,6 +192,7 @@ centos-latest:</td>
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<td class="diff-line-num 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">
193
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<td class="diff-line-num new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install tar</span></span>
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<td class="diff-line-num old_line" data-linenumber="194" 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">
194
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<td class="diff-line-num new_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">
193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install which</span></span>
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<td class="diff-line-num old_line" data-linenumber="195" 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">
195
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<td class="diff-line-num new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install wget</span></span>
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<td class="diff-line-num new old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">yum -y install gcc-gfortran</span></span>
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<td class="diff-line-num old_line" data-linenumber="196" 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">
196
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<td class="diff-line-num new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tar -xzvf ncbi-blast*-x64-linux.tar.gz</span></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cp ncbi-blast*/bin/blastp $HOME</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">@@ -205,7 +205,6 @@ centos-latest:</td>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">echo "start proteinortho tests"</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make clean</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make test</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="yaml"> </span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="yaml"><span class="na" style="color: #008080;">code_quality</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="yaml"> <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker:stable</span></span>
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<li id="e52fa9f6246a270e3b0a6a888a797d22f02e2532">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#e52fa9f6246a270e3b0a6a888a797d22f02e2532"><strong>src/proteinortho_ffadj_mcs.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">python3</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env python</span></span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">exit</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">maxsize</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">copy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deepcopy</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">@@ -8,9 +8,6 @@ from random import randint</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">math</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ceil</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">log</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">ALPHA</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BothStrands</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">x</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">@@ -59,9 +56,9 @@ class Run:</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'G1:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s G2:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s<span class="idiff left"> (</span></span><span class="si" style="color: #d14;"><span class="idiff">%.5</span></span><span class="s" style="color: #d14;"><span class="idiff right">f)</span>'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'G1:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s G2:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ALPHA</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readDistsAndOrder</span><span class="p">(</span><span class="n" style="color: #333;">dist_file</span><span class="p">,</span> <span class="n" style="color: #333;">edgeThreshold</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">@@ -133,11 +130,11 @@ def sort_genome(chrom_pos):</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">telomeres</span><span class="p">,</span> <span class="n" style="color: #333;">g</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">run</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">runList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="360" 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">@@ -363,7 +360,7 @@ def replaceByNew(g1_runs, g2_runs, i, j, r_old, r_new):</td>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">newRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="452" 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">@@ -455,6 +452,7 @@ def doMatching(g1, g2, g1_runs, g2_runs, m, runList):</td>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Divided overlapping run in </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s and </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">replaceByNew</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r_new</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">@@ -480,10 +478,10 @@ def doMatching(g1, g2, g1_runs, g2_runs, m, runList):</td>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">newRuns</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mergeRuns</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">,</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mergeRuns</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">,</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"> <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -504,9 +502,9 @@ def mergeRuns(mod_g1, g1, g2, g1_runs, g2_runs, runList, alreadyMatched):</td>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># points (mod_g1) can be processed.</span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">product</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">difference</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="LC507" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python"> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">difference</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]),</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</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">@@ -538,7 +536,7 @@ def mergeRuns(mod_g1, g1, g2, g1_runs, g2_runs, runList, alreadyMatched):</td>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">alreadyMatched</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># redo matching in case r1 xor r2 were not in matching before</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">[</span><span class="n" style="color: #333;">x</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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543
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># actually, both are already matched</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">@@ -548,7 +546,7 @@ def mergeRuns(mod_g1, g1, g2, g1_runs, g2_runs, runList, alreadyMatched):</td>
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># none is matched</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"> <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">)</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[]</span></span>
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -567,7 +565,7 @@ def removeSingleGenes(genome, genome_runs):</td>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">del_res</span><span class="p">,</span> <span class="n" style="color: #333;">mod_res</span></span>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">g2dists</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g1i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">dists</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g2j</span><span class="p">,</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="583" 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">@@ -585,11 +583,12 @@ def findRandomRunSequence(g1, g2, dists, topXperCent):</td>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getAllRuns</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Found </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s runs.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sort</span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">runList</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"> <span class="n" style="color: #333;">runList</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">runList</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">noOfAdjacencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">([</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;">ALPHA</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;">ALPHA</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">noOfAdjacencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">([</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;">alpha</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;">alpha</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">noOfAdjacencies</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">randPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">noOfAdjacencies</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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">@@ -601,7 +600,7 @@ def findRandomRunSequence(g1, g2, dists, topXperCent):</td>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">mx</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">mx</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># update run list</span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">doMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">mx</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"> <span class="n" style="color: #333;">doMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">mx</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">del_g1</span><span class="p">,</span> <span class="n" style="color: #333;">new_mod_g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeSingleGenes</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">del_g1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Zombie genes removed from G1: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">del_g1</span><span class="p">)))</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="630" 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">@@ -631,7 +630,7 @@ def findRandomRunSequence(g1, g2, dists, topXperCent):</td>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"> <span class="n" style="color: #333;">mod_g1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">]</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="LC631" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># merge runs</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">mx</span><span class="p">,</span> <span class="n" style="color: #333;">mod_g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mergeRuns</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">runList</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"> <span class="n" style="color: #333;">runList</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Matching finished. Longest run size is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">res</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">@@ -642,7 +641,7 @@ def findRandomRunSequence(g1, g2, dists, topXperCent):</td>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">repeatMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">repMatching</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">minCsSize</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">minCsSize</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_mod</span></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">g2_mod_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2_mod</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">@@ -680,7 +679,7 @@ def repeatMatching(g1, g2, g1_mod, g2_mod, g1_runs, g2_runs, dists, repMatching,</td>
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679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">noReps</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alpha</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">checkMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Obtained </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s adjacencies in matching of size </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s from iteration </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="793" 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="792" 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">@@ -793,7 +792,6 @@ if __name__ == '__main__':</td>
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793
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"> <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--alpha'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'F'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"> <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'dist_file'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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796
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="python"> <span class="n" style="color: #333;">AlPHA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">alpha</span></span>
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">repeat_matching</span></span>
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798
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">repMatching</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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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</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">@@ -802,14 +800,16 @@ if __name__ == '__main__':</td>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%(levelname)</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%(asctime)</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">++ </span><span class="si" style="color: #d14;">%(message)</span><span class="s" style="color: #d14;">s"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python"> <span class="n" style="color: #333;">multiChrom</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDistsAndOrder</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dist_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge_weight_threshold</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC805" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">greedy</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python"> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">greedy</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">alpha</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python"> <span class="n" style="color: #333;">checkMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># calculate number of breakpoints only from result of the first matching</span></span>
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="python"> <span class="n" style="color: #333;">bkp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repeatMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span></span>
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812
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">repMatching</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_cs_size</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">greedy</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="python"> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">repMatching</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_cs_size</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">greedy</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">alpha</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"> <span class="n" style="color: #333;">selectedRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns_new</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -833,3 +833,4 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'#bkp</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">#edg</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">adj</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">edg'</span><span class="p">)</span></span>
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835
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.6</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.6</span><span class="s" style="color: #d14;">f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">bkp</span><span class="p">,</span> <span class="n" style="color: #333;">edg</span><span class="p">,</span> <span class="n" style="color: #333;">wAdj</span><span class="p">,</span> <span class="n" style="color: #333;">wEdg</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#baed8b8088767318f56f01f49bec7ce10b85899f"><strong>src/proteinortho_history.pl</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#pk</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" 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="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This file is part of proteinortho.</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># (C) 2009 Marcus Lechner</span></span>
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<pre style="margin: 0;">+<span id="LC7" 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="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># proteinortho is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># it under the terms of the GNU General Public License as published</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># by the Free Software Foundation; either version 2, or (at your</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC12" 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="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># proteinortho is distributed in the hope that it will be useful, but</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># General Public License for more details.</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" 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="LC18" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU General Public License</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># along with proteinortho; see the file COPYING. If not, write to the</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Free Software Foundation, Inc., 59 Temple Place - Suite 330,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Boston, MA 02111-1307, USA. </span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" 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="LC23" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC24" 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="LC25" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># About</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" 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="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 1</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 11-11-2019</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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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">POSIX</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"><span class="s2" style="color: #d14;">proteinortho_history.pl reports the history of a (or a pair of) gene/protein(s).</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"><span class="s2" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"><span class="s2" style="color: #d14;">SYNOPSIS</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"><span class="s2" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"><span class="s2" style="color: #d14;">proteinortho_history.pl (-project=myproject) QUERY (FASTA1 FASTA2 ...)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"><span class="s2" style="color: #d14;"> QUERY A string of a single gene/protein or 2 separated by a comma or a whitespace (the input is escaped using quotemeta, use -noquotemeta to avoid this)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="perl"><span class="s2" style="color: #d14;"> -project=MYPROJECT The project name (as specified in proteinortho with -project) (default:auto detect in the current directory)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step=[123] (optional) If specified more optput is printed (to STDOUT) for the given step:</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step=1 : search for the given fasta sequence in the input fasta files</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step=2 : search in the *.blast-graph</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step=3 : search in the *.proteinortho file </span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"><span class="s2" style="color: #d14;"> -step=all : prints everything of above to STDOUT</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"><span class="s2" style="color: #d14;"> FASTA* (optional) input fasta files </span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"><span class="s2" style="color: #d14;"> -noquotemeta, -E (optional) If set, then the query will not be escaped.</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"><span class="s2" style="color: #d14;"> -plain, -p, -notableformat (optional) If -step= is set too, then the tables are not formatted and a plain csv is printed instead. </span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"><span class="s2" style="color: #d14;"> -delim= (optional) Defines the delimiter character for spliting the query (if you want to search for 2 genes/proteins)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"><span class="s2" style="color: #d14;"> NOTE: if you use the -keep option and you have the project_cache_proteinortho/ directory, this program additionally searches for all blast hits.</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"><span class="p">";</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">tput cols</span><span class="p">`;</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl"><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$split_delim</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">[:</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">]</span><span class="p">";</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@spl_header</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$last_isHeaderLine</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="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$query</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$query_esc</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$help</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">myproject</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$delim</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">[, ]</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$do_quotemeta</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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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$notableformat</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ARGViddone</span><span class="o" style="font-weight: 600;">=[]</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ARGViddone_counter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ARGV</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="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</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl"> </span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(help|h)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$help</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?project=?(.*)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span><span class="p">;</span><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$project</span><span class="p">);</span><span class="nv" style="color: #008080;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?step=?([123]|(all))$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span><span class="p">;</span><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="p">);</span><span class="nv" style="color: #008080;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?delim=?(.*)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$delim</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span><span class="p">;</span><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$delim</span><span class="p">);</span><span class="nv" style="color: #008080;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?noquotemeta$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$do_quotemeta</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;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?E$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$do_quotemeta</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;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?notableformat$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$notableformat</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;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?plain$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$notableformat</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;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?p$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$notableformat</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;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^-.+/</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ERROR: invalid option </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">)){</span><span class="nv" style="color: #008080;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="nv" style="color: #008080;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$ARGViddone_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="perl"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="perl"><span class="p">}</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="perl"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$project_corrected</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$help</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="perl"><span class="p">}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$fail</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" 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;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">)){</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="perl"> <span class="nv" style="color: #008080;">$fail</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="s2" style="color: #d14;">ERROR: no QUERY provided!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="perl"><span class="p">}</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" 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="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.blast-graph</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.proteinortho.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.proteinortho-graph</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">d</span> <span class="p">"</span><span class="s2" style="color: #d14;">proteinortho_cache_</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$project</span><span class="p">){</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="perl"> <span class="nv" style="color: #008080;">@blastglob</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="s2" style="color: #d14;">*.blast-graph</span><span class="p">");</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="perl"> <span class="nv" style="color: #008080;">@proteinorthoglob</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="s2" style="color: #d14;">*.proteinortho.tsv</span><span class="p">");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="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;">@blastglob</span><span class="p">)</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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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl"> <span class="nv" style="color: #008080;">$project_corrected</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$project</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$blastglob</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span><span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/.blast-graph$//g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@proteinorthoglob</span><span class="p">)</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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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="perl"> <span class="nv" style="color: #008080;">$project_corrected</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$project</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="perl"> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$proteinorthoglob</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span><span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/.blast-graph$//g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"> <span class="nv" style="color: #008080;">$fail</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="s2" style="color: #d14;">ERROR: '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' files not found, make sure you are in the directory with the proteinortho output! Specify the project name (prefix) with -project=... </span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="perl"> <span class="p">}</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="p">}</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="perl"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$do_quotemeta</span><span class="p">){</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="perl"> <span class="nv" style="color: #008080;">$query_esc</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;">$query</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="perl"> <span class="nv" style="color: #008080;">$query_esc</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\\([, ])/$1/</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="perl"> <span class="nv" style="color: #008080;">$query_esc</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\\($delim)/$1/</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nv" style="color: #008080;">$query_esc</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">(escaped the input query '</span><span class="si" style="color: #d14;">$query</span><span class="s2" style="color: #d14;">' -> '</span><span class="si" style="color: #d14;">$query_esc</span><span class="s2" style="color: #d14;">')</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="perl"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="perl"> <span class="nv" style="color: #008080;">$query_esc</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="perl"><span class="p">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="perl"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@query_split</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="nv" style="color: #008080;">$delim</span><span class="p">,</span><span class="nv" style="color: #008080;">$query_esc</span><span class="p">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@query_split_noesc</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="nv" style="color: #008080;">$delim</span><span class="p">,</span><span class="nv" style="color: #008080;">$query</span><span class="p">);</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="perl"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@query_split</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="perl"> <span class="nv" style="color: #008080;">$fail</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="s2" style="color: #d14;">ERROR: the QUERY contains too many delimiters ([, ]), specify the delimiter character with -delim=... !</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="perl"><span class="p">}</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="perl"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$fail</span><span class="p">){</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$fail</span><span class="p">;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="perl"><span class="p">}</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="perl"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">A short history of '</span><span class="p">";</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@query_split</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">' in '</span><span class="si" style="color: #d14;">$project</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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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="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;">:::::::[ input files ]::::::::::::::::</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># input files</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$did_found_a_in_input</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="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$did_found_b_in_input</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="perl"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">1</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">all</span><span class="p">"){</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="perl"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$ARGViddone_counter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ARGV</span><span class="p">)</span> <span class="p">){</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">checking the input fasta files...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$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;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGViddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$query</span><span class="p">){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> ! WARNING ! did not find file '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">', proceeding anyway...</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">r</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">! WARNING ! cannot read '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">', proceeding anyway...</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$ARGV</span><span class="sb" style="color: #d14;">[</span><span class="si" style="color: #d14;">$v</span><span class="sb" style="color: #d14;">] 2>/dev/null</span><span class="p">`;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_result</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</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;">$did_found_a_in_input</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">! WARNING ! found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' again in </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">. (proteinortho can handle this) </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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># did not found the query in this file ...</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</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="nv" style="color: #008080;">$did_found_a_in_input</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' in </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span 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="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="perl"> <span class="nv" style="color: #008080;">$did_found_a_in_input</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">`</span><span class="sb" style="color: #d14;">proteinortho_grab_proteins.pl -E '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$ARGV</span><span class="sb" style="color: #d14;">[</span><span class="si" style="color: #d14;">$v</span><span class="sb" style="color: #d14;">]</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</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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<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 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;">! ERROR ! found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' multiple times in </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">. This seems dangerous, make sure there are no duplicates present in your fasta files ! </span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">`</span><span class="sb" style="color: #d14;">proteinortho_grab_proteins.pl -E '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$ARGV</span><span class="sb" style="color: #d14;">[</span><span class="si" style="color: #d14;">$v</span><span class="sb" style="color: #d14;">]</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="perl"> <span class="p">}</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="perl"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@query_split</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$ARGV</span><span class="sb" style="color: #d14;">[</span><span class="si" style="color: #d14;">$v</span><span class="sb" style="color: #d14;">] 2>/dev/null</span><span class="p">`;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_result</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</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;">$did_found_b_in_input</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">! WARNING ! found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' again in </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">. (proteinortho can handle this) </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="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$result</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="perl"> <span class="p">}</span></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;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># did not found the query in this file ...</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</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="nv" style="color: #008080;">$did_found_b_in_input</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' in </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span 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="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="perl"> <span class="nv" style="color: #008080;">$did_found_b_in_input</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">`</span><span class="sb" style="color: #d14;">proteinortho_grab_proteins.pl -E '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$ARGV</span><span class="sb" style="color: #d14;">[</span><span class="si" style="color: #d14;">$v</span><span class="sb" style="color: #d14;">]</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_result</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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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="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;">! ERROR ! found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' multiple times in </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">. This seems dangerous, make sure there are no duplicates present in your fasta files ! </span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">`</span><span class="sb" style="color: #d14;">proteinortho_grab_proteins.pl -E '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$ARGV</span><span class="sb" style="color: #d14;">[</span><span class="si" style="color: #d14;">$v</span><span class="sb" style="color: #d14;">]</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="perl"> <span class="p">}</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="perl"> <span class="p">}</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="perl"> <span class="p">}</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$did_found_a_in_input</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" 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;">! ERROR ! did not found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' in the provided fasta files...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@query_split</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$did_found_b_in_input</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" 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;">! ERROR ! did not found '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' in the provided fasta files...</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="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<pre style="margin: 0;">+<span id="LC212" 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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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" 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;">input fasta files are not provided: skipping</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="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</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;">(use -step=1 for more details)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" 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;">:::::::[ all versus all blast ]:::::::</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
219
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<pre style="margin: 0;">+<span id="LC219" 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="LC220" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># step 2 blast-graph</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># TODO the single blast graph ... </span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$proteinortho_cache</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_a_all_blast_hits</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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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_b_all_blast_hits</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_ab_all_blast_hits</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="LC227" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_a_aRBH_hits</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_b_aRBH_hits</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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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_ab_aRBH_hits</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">2</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">all</span><span class="p">"){</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC233" 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;">d</span> <span class="p">"</span><span class="s2" style="color: #d14;">proteinortho_cache_</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$project</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="perl"> <span class="nv" style="color: #008080;">$proteinortho_cache</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="LC235" 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;">checking all blast files in 'proteinortho_cache_</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' proteinortho_cache_</span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">/*.vs.* 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_a_all_blast_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC240" 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 query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_a_all_blast_hits</span><span class="s2" style="color: #d14;"> hit(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">pident</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">length</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">mismatch</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qend</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">send</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">evalue</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">bitscore</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</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;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@query_split</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</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="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' proteinortho_cache_</span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">/*.vs.* 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_b_all_blast_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">the query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_b_all_blast_hits</span><span class="s2" style="color: #d14;"> hit(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">pident</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">length</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">mismatch</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qend</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">send</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">evalue</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">bitscore</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nHE '(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)|(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)' proteinortho_cache_</span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">/*.vs.* 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_ab_all_blast_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">both queries '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' have </span><span class="si" style="color: #d14;">$num_ab_all_blast_hits</span><span class="s2" style="color: #d14;"> hit(s) with each other use -step=2 for more details).</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="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">pident</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">length</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">mismatch</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qend</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">send</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">evalue</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">bitscore</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="perl"></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print "grep -nH '(\\b$query_split[0]\\b\\t\\b$query_split[1]\\b)|(\\b$query_split[1]\\b\\t\\b$query_split[0]\\b)' proteinortho_cache_$project/*.vs.* 2>/dev/null";</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="perl"> <span class="p">}</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="perl"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="s2" style="color: #d14;">*.vs.*</span><span class="p">")){</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="perl"> <span class="nv" style="color: #008080;">$proteinortho_cache</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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262
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<pre style="margin: 0;">+<span id="LC262" 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;">checking all blast files...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' *.vs.* 2>/dev/null</span><span class="p">`;</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_a_all_blast_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" 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 query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_a_all_blast_hits</span><span class="s2" style="color: #d14;"> hit(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">pident</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">length</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">mismatch</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qend</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">send</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">evalue</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">bitscore</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@query_split</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' *.vs.* 2>/dev/null</span><span class="p">`;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_b_all_blast_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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<pre style="margin: 0;">+<span id="LC275" 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 query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_b_all_blast_hits</span><span class="s2" style="color: #d14;"> hit(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">pident</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">length</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">mismatch</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qend</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">send</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">evalue</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">bitscore</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="perl"></span>
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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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nHE '(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)|(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)' *.vs.* 2>/dev/null</span><span class="p">`;</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_ab_all_blast_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">both queries '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' have </span><span class="si" style="color: #d14;">$num_ab_all_blast_hits</span><span class="s2" style="color: #d14;"> hit(s) with each other use -step=2 for more details).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sseqid</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">pident</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">length</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">mismatch</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">qend</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">sstart</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">send</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">evalue</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">bitscore</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="perl"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print "grep -nH '(\\b$query_split[0]\\b\\t\\b$query_split[1]\\b)|(\\b$query_split[1]\\b\\t\\b$query_split[0]\\b)' *.vs.* 2>/dev/null";</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="perl"> <span class="p">}</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" 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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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" 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;">did not found the temporary files *.vs.* neither in 'proteinortho_cache_</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/' nor in the current directory. If you want to analyse all blast files please use '-keep' option with proteinortho or provide the *.vs.* files in the current directory...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" 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;">:::::::[ reciprocal best hit ]::::::::</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
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<pre style="margin: 0;">+<span id="LC292" 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;">e</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.blast-graph</span><span class="p">"){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<pre style="margin: 0;">+<span id="LC293" 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;">checking the blast-graph '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.blast-graph' (reciprocal adaptive best hit graph)...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="perl"></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.blast-graph 2>/dev/null</span><span class="p">`;</span></span>
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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;">$num_a_aRBH_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="perl"></span>
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298
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<pre style="margin: 0;">+<span id="LC298" 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 query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_a_aRBH_hits</span><span class="s2" style="color: #d14;"> reciprocal hit(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",`</span><span class="sb" style="color: #d14;">head -n2 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.blast-graph |tail -n1| perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="perl"></span>
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301
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<pre style="margin: 0;">+<span id="LC301" 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="nv" style="color: #008080;">@query_split</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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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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<pre style="margin: 0;">+<span id="LC303" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.blast-graph 2>/dev/null</span><span class="p">`;</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_b_aRBH_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="perl"></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">the query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_b_aRBH_hits</span><span class="s2" style="color: #d14;"> reciprocal hit(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",`</span><span class="sb" style="color: #d14;">head -n2 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.blast-graph |tail -n1| perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nHE '(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)|(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.blast-graph 2>/dev/null</span><span class="p">`;</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_ab_aRBH_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">both queries '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' have </span><span class="si" style="color: #d14;">$num_ab_aRBH_hits</span><span class="s2" style="color: #d14;"> reciprocal hit(s) with each other.</span><span class="se" style="color: #d14;">\n</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 class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",`</span><span class="sb" style="color: #d14;">head -n2 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.blast-graph |tail -n1| perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="perl"> <span class="p">}</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">did not found the blast-graph '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.blast-graph': skipping...</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="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</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;">(use -step=2 for more details)</span><span class="se" style="color: #d14;">\n</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 class="p">}</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="perl"></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;">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;">:::::::[ clustering ]:::::::::::::::::</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># step 3 proteinortho</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_a_cluster_hits</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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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_b_cluster_hits</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_ab_cluster_hits</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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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_a_cluster_groups</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_b_cluster_groups</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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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$num_ab_cluster_groups</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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333
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">3</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">all</span><span class="p">"){</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC336" 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;">e</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.proteinortho-graph</span><span class="p">"){</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">checking the proteinortho-graph '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho-graph' (result of the clustering)...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho-graph 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_a_cluster_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="perl"></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">the query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_a_cluster_hits</span><span class="s2" style="color: #d14;"> putative ortholog(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">echo '# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">'|tr -d '</span><span class="se" style="color: #d14;">\n</span><span class="sb" style="color: #d14;">'; head -n2 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho-graph| tail -n1 | sed 's/#//g'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC345" 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="nv" style="color: #008080;">@query_split</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho-graph 2>/dev/null</span><span class="p">`;</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_b_cluster_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">the query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' got </span><span class="si" style="color: #d14;">$num_b_cluster_hits</span><span class="s2" style="color: #d14;"> putative ortholog(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">echo '# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">'|tr -d '</span><span class="se" style="color: #d14;">\n</span><span class="sb" style="color: #d14;">'; head -n2 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho-graph| tail -n1 | sed 's/#//g'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nHE '(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)|(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">t</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho-graph 2>/dev/null</span><span class="p">`;</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_ab_cluster_hits</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="perl"></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_ab_cluster_hits</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">both queries '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' are putative ortholog(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">echo '# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">'|tr -d '</span><span class="se" style="color: #d14;">\n</span><span class="sb" style="color: #d14;">'; head -n2 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho-graph| tail -n1 | sed 's/#//g'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" 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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<td class="diff-line-num new new_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
360
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<pre style="margin: 0;">+<span id="LC360" 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;">both queries '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' are NOT putative ortholog(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC365" 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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<pre style="margin: 0;">+<span id="LC366" 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;">did not found the proteinortho-graph '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho-graph': skipping...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="perl"> <span class="p">}</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">:::::::[ clustering groups ]::::::::::</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="perl"></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="perl"></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.proteinortho.tsv</span><span class="p">"){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
372
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<pre style="margin: 0;">+<span id="LC372" 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;">checking the proteinortho.tsv file '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho.tsv' (result of the clustering)...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho.tsv 2>/dev/null</span><span class="p">`;</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_a_cluster_groups</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="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 query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' is part of </span><span class="si" style="color: #d14;">$num_a_cluster_groups</span><span class="s2" style="color: #d14;"> group(s) of putative orthologs.</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="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;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">head -n1 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho.tsv | perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="perl"></span>
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380
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<pre style="margin: 0;">+<span id="LC380" 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="nv" style="color: #008080;">@query_split</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="perl"></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="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho.tsv 2>/dev/null</span><span class="p">`;</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_b_cluster_groups</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">the query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' is part of </span><span class="si" style="color: #d14;">$num_b_cluster_groups</span><span class="s2" style="color: #d14;"> group(s) of putative orthologs.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">head -n1 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho.tsv | perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nHE '(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b.*</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)|(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b.*</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho.tsv 2>/dev/null</span><span class="p">`;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_ab_cluster_groups</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">both queries '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' have </span><span class="si" style="color: #d14;">$num_ab_cluster_groups</span><span class="s2" style="color: #d14;"> group(s) in common.</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="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">head -n1 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho.tsv | perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="perl"></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="perl"> <span class="p">}</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="perl"></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.proteinortho</span><span class="p">"){</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">checking the proteinortho file '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho' (result of the clustering)...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="perl"></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_a_cluster_groups</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="perl"></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">the query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' is part of </span><span class="si" style="color: #d14;">$num_a_cluster_groups</span><span class="s2" style="color: #d14;"> group(s) of putative orthologs.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">head -n1 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho | perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@query_split</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nH '</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_b_cluster_groups</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC410" 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 query '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' is part of </span><span class="si" style="color: #d14;">$num_b_cluster_groups</span><span class="s2" style="color: #d14;"> group(s) of putative orthologs.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">head -n1 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho | perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="413" style="width: 35px; color: rgba(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="LC413" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">grep -nHE '(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b.*</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)|(</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[1]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b.*</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b</span><span class="si" style="color: #d14;">$query_split</span><span class="sb" style="color: #d14;">[0]</span><span class="se" style="color: #d14;">\\</span><span class="sb" style="color: #d14;">b)' </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="perl"> <span class="nv" style="color: #008080;">$num_ab_cluster_groups</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">);</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="perl"></span>
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416
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<pre style="margin: 0;">+<span id="LC416" 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;">both queries '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' and '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_split_noesc</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' have </span><span class="si" style="color: #d14;">$num_ab_cluster_groups</span><span class="s2" style="color: #d14;"> group(s) in common.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</span><span class="p">"){</span><span class="nv" style="color: #008080;">$result</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">head -n1 </span><span class="si" style="color: #d14;">$project</span><span class="sb" style="color: #d14;">.proteinortho | perl -lne 'chomp;s/#//g;print "# file</span><span class="se" style="color: #d14;">\t</span><span class="sb" style="color: #d14;">line</span><span class="se" style="color: #d14;">\t</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$_</span><span class="sb" style="color: #d14;">"'</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$result</span><span class="p">;</span><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">)){</span><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="perl"></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="perl"> <span class="p">}</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="perl"></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">did not found the proteinortho.tsv '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho.tsv': skipping...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="perl"> <span class="p">}</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="perl"></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">none</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;">(use -step=3 for more details)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="perl"></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="perl"><span class="p">}</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" 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;">:::::::[ summary ]::::::::::::::::::::</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
429
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<pre style="margin: 0;">+<span id="LC429" 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="nv" style="color: #008080;">@query_split</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$did_found_b_in_input</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$did_found_a_in_input</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Found both queries in the input files.</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Did found the two queries in the input files...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);}</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$proteinortho_cache</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_ab_all_blast_hits</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Both queries hit each other</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Sadly, the two queries did not hit each other using the blast algorithm...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_ab_aRBH_hits</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;"> AND they are adaptive reciprocal best hits too.</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</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;"> but they are NOT adaptive reciprocal best hits...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</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="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
434
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<pre style="margin: 0;">+<span id="LC434" 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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<td class="diff-line-num new new_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_ab_aRBH_hits</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Furthermore, Both queries are adaptive reciprocal best hits.</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Sadly, both queries are NOT adaptive reciprocal best hits...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);}</span> </span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_ab_cluster_groups</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;">Finally, both queries are putative orthologs, since they occure in the same group after the clustering step.</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</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;">Sadly, both queries are NOT putative orthologs, since they are not occuring in the same group after the clustering step....</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</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="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
438
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<pre style="margin: 0;">+<span id="LC438" 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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<td class="diff-line-num new new_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$did_found_a_in_input</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Found the query in the input files.</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">I did NOT find the query in the input files...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);}</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$proteinortho_cache</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_a_all_blast_hits</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The query hit </span><span class="si" style="color: #d14;">$num_a_all_blast_hits</span><span class="s2" style="color: #d14;"> other protein(s)/gene(s) (blast-graph)</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</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;">the query did not hit anything (blast-graph)...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</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="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_a_aRBH_hits</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> AND </span><span class="si" style="color: #d14;">$num_a_aRBH_hits</span><span class="s2" style="color: #d14;"> of these hits are adaptive reciprocal best hits too.</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</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;"> BUT none of these hits are adaptive reciprocal best hits...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</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="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
443
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<pre style="margin: 0;">+<span id="LC443" 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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<td class="diff-line-num new new_line" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_a_aRBH_hits</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The query is part of the adaptive reciprocal best hit graph.</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The query is NOT part of the adaptive reciprocal best hit graph...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);}</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$num_a_cluster_groups</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;">Furthermore, the query is a putative ortholog with </span><span class="si" style="color: #d14;">$num_a_cluster_hits</span><span class="s2" style="color: #d14;"> other protein(s)/gene(s)</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</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;">Sadly, the query is NOT a putative ortholog of any other protein(s)/gene(s)....</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);}</span> </span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="perl"><span class="p">}</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC449" 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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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="perl"></span>
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451
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<pre style="margin: 0;">+<span id="LC451" 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;">WARNING: The project '</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$project_corrected</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">' was not found, I automatically detected '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">' ! (Specify the project name (prefix) with -project=...)</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="perl"></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="perl"></span>
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455
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="perl"></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">processLine</span><span class="p">{</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="perl"> <span class="nv" style="color: #008080;">$_</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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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$notableformat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$_</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="perl"></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="perl"></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$split_delim</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl_t</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">$_</span><span class="p">);</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl_c</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nv" style="color: #008080;">$_</span><span class="p">);</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl_s</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;">$_</span><span class="p">);</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
470
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<pre style="margin: 0;">+<span id="LC470" 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="nv" style="color: #008080;">@spl_t</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_c</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_s</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</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="LC471" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC472" 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="nv" style="color: #008080;">@spl_t</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_c</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_t</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_s</span> <span class="p">){</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@spl_t</span><span class="p">;</span> <span class="nv" style="color: #008080;">$split_delim</span><span class="o" style="font-weight: 600;">=</span><span class="p">'</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s1" style="color: #d14;">t</span><span class="p">';}</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_c</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_t</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_c</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_s</span> <span class="p">){</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@spl_c</span><span class="p">;</span> <span class="nv" style="color: #008080;">$split_delim</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">,</span><span class="p">";}</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_s</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_c</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_s</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_t</span> <span class="p">){</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@spl_s</span><span class="p">;</span> <span class="nv" style="color: #008080;">$split_delim</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>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC476" 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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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl</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;">$split_delim</span><span class="p">,</span><span class="nv" style="color: #008080;">$_</span><span class="p">);</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="perl"> <span class="p">}</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl_backup</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@spl</span><span class="p">;</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="perl"></span>
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482
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<pre style="margin: 0;">+<span id="LC482" 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="nv" style="color: #008080;">@spl_header</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="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_header</span><span class="p">){</span><span class="nv" style="color: #008080;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="p">){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">$spl</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^# ?//g</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@spl</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Corrected minimum table width: -w=</span><span class="si" style="color: #d14;">$maxNumOfCharsInOneLine</span><span class="s2" style="color: #d14;"> such that at least 1 character per column is displayed.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="perl"></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sumOfCharsLine</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">));</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isHeaderLine</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># is a header row </span></span>
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<td class="diff-line-num new new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="nv" style="color: #008080;">$sumOfCharsLine</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># shave of chars from widest cell</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="perl"> <span class="nv" style="color: #008080;">$max_l</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="perl"> <span class="nv" style="color: #008080;">@max_l_is</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</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;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$max_l</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span><span class="nv" style="color: #008080;">$max_l</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">];</span><span class="nv" style="color: #008080;">@max_l_is</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@max_l_is</span><span class="p">,</span><span class="nv" style="color: #008080;">$i</span><span class="p">)}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$max_l</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@max_l_is</span><span class="p">,</span><span class="nv" style="color: #008080;">$i</span><span class="p">)}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="perl"> <span class="p">}</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</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;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@max_l_is</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</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 class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">...</span><span class="p">"</span> <span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]])</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">...</span><span class="p">"</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="perl"> <span class="p">}</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</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;">$spl_backup</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]])</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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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="perl"> <span class="p">}</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="perl"> <span class="p">}</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sumOfCharsLine</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="perl"></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="perl"></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="nv" style="color: #008080;">$sumOfCharsLine</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># add of chars to smallest cell</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="perl"> <span class="nv" style="color: #008080;">$min_l</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="perl"> <span class="nv" style="color: #008080;">@min_l_is</span><span class="p">;</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</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;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$min_l</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span><span class="nv" style="color: #008080;">$min_l</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">];</span><span class="nv" style="color: #008080;">@min_l_is</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@min_l_is</span><span class="p">,</span><span class="nv" style="color: #008080;">$i</span><span class="p">)}</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="perl"> <span class="p">}</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</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;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@min_l_is</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="perl"></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="perl"> <span class="nv" style="color: #008080;">$leftPad</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="perl"> <span class="nv" style="color: #008080;">$rightPad</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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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/( +)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$rightPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/^( +)/</span><span class="p">){</span><span class="nv" style="color: #008080;">$leftPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="perl"></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$leftPad</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$rightPad</span> <span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</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;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">";</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="perl"> <span class="p">}</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="perl"> </span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="perl"> <span class="p">}</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sumOfCharsLine</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">));</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="perl"> <span class="p">}</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="perl"></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@spl</span><span class="p">;</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="perl"></span>
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533
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<pre style="margin: 0;">+<span id="LC533" 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;"># is not headerline -> do the same as in headerline</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="perl"> </span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_header</span><span class="p">){</span><span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;}</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="perl"></span>
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537
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<pre style="margin: 0;">+<span id="LC537" 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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl_header</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span> <span class="c1" style="color: #998; font-style: italic;"># add pads</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="perl"> <span class="nv" style="color: #008080;">$leftPad</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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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="perl"> <span class="nv" style="color: #008080;">$rightPad</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/( +)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$rightPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/^( +)/</span><span class="p">){</span><span class="nv" style="color: #008080;">$leftPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="perl"></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$leftPad</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$rightPad</span> <span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">];</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">";</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="perl"> <span class="p">}</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="perl"> <span class="p">}</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">></span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl_header</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span> <span class="c1" style="color: #998; font-style: italic;"># trim</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">],</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">...</span><span class="p">"</span> <span class="p">){</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">])</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">...</span><span class="p">"</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl_backup</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">])</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="perl"> <span class="p">}</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="perl"> <span class="p">}</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="perl"></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isHeaderLine</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$last_isHeaderLine</span> <span class="p">){</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">|</span><span class="p">",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">);</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\|/+/g</span><span class="p">;</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^+]/-/g</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">|</span><span class="p">",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isHeaderLine</span> <span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">|</span><span class="p">",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">);</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\|/+/g</span><span class="p">;</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^+]/-/g</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp</span><span class="p">";}</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="perl"> <span class="nv" style="color: #008080;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$isHeaderLine</span><span class="p">;</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="perl"> <span class="nv" style="color: #008080;">$isHeaderLine</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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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="perl"></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="perl"></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="perl"><span class="p">}</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="perl"></span></pre>
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<li id="1486be463578edbd60b13d54cd9e0d2b9d4ecd99">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/83071ae5ce0d7816bbf6ec8d0ba0ccae976ebc7e#1486be463578edbd60b13d54cd9e0d2b9d4ecd99"><strong>src/proteinortho_summary.pl</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#pk</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This file is part of proteinortho.</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># (C) 2009 Marcus Lechner</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># </span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># proteinortho is free software; you can redistribute it and/or modify</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># it under the terms of the GNU General Public License as published</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># by the Free Software Foundation; either version 2, or (at your</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># option) any later version.</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># proteinortho is distributed in the hope that it will be useful, but</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># General Public License for more details.</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" 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="LC18" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># along with proteinortho; see the file COPYING. If not, write to the</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Free Software Foundation, Inc., 59 Temple Place - Suite 330,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Boston, MA 02111-1307, USA. </span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" 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="LC23" class="line" lang="perl"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># About</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" 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="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 1</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 11-12-2019</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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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">POSIX</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"><span class="s2" style="color: #d14;">proteinortho_summary.pl produces a summary on species level.</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"><span class="s2" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"><span class="s2" style="color: #d14;">SYNOPSIS</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"><span class="s2" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"><span class="s2" style="color: #d14;">proteinortho_summary.pl (options) GRAPH (GRAPH2)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"><span class="s2" style="color: #d14;"> GRAPH Path to the *.proteinortho-graph or *.blast-graph file generated by proteinortho. </span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"><span class="s2" style="color: #d14;"> GRAPH2 (optional) If you provide a blast-graph AND a proteinortho-graph, the difference is calculated (GRAPH - GRAPH2)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"><span class="s2" style="color: #d14;"> Note: The *.proteinortho.tsv file does not work here (use the proteinortho-graph file)</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"><span class="s2" style="color: #d14;"> OPTIONS</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"><span class="s2" style="color: #d14;"> -format,-f enables the table formatting instead of the plain csv output.</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"><span class="p">";</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$graphfilenameA</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$graphfilenameB</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$notableformat</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$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;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(help|h)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$help</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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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(format|f)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$notableformat</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="LC63" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^-.+/</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ERROR: invalid option </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$graphfilenameA</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="nv" style="color: #008080;">$graphfilenameA</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$graphfilenameB</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="nv" style="color: #008080;">$graphfilenameB</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];}</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"><span class="p">}</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$help</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$fail</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$graphfilenameA</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="perl"> <span class="nv" style="color: #008080;">$fail</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="s2" style="color: #d14;">ERROR: GRAPH not provided!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$fail</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$fail</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">tput cols</span><span class="p">`;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="perl"><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$split_delim</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">[:</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">]</span><span class="p">";</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@spl_header</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$noheader</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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="perl"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="perl"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" 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;">species_matrix</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" 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;">species_matrix_pow2</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="perl"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="perl"><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;">$FH</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="p">",</span><span class="nv" style="color: #008080;">$graphfilenameA</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span> <span class="vg" style="color: #008080;">$!</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;"># file_a file_b</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;"># a b evalue_ab bitscore_ab evalue_ba bitscore_ba</span><span class="p">"){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">$_</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" 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;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@arr</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="perl"> <span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"> <span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="perl"> <span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^# ?//g</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@arr</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span><span class="p">){</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}</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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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}</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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112
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<pre style="margin: 0;">+<span id="LC112" 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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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"> <span class="p">}</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@arr</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">){</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] Error: wrong fromat... Please make sure you only provide *.blast-graph or *.proteinortho-graph files as input...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="perl"> <span class="p">}</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="perl"><span class="p">}</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="perl"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$graphfilenameB</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="p">",</span><span class="nv" style="color: #008080;">$graphfilenameB</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span> <span class="vg" style="color: #008080;">$!</span><span class="p">;</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" 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;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</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="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">$_</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</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="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@arr</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="perl"> <span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="perl"> <span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="perl"> <span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^# ?//g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</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;">ne</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 new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="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;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}</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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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}</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="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}</span> <span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$currentSpeciesB</span><span class="p">}{</span><span class="nv" style="color: #008080;">$currentSpeciesA</span><span class="p">}</span> <span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="perl"> <span class="p">}</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="perl"> <span class="p">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="perl"> <span class="p">}</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="perl"><span class="p">}</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@keys</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">sort</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">species_matrix</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl"><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># The adjacency matrix, the number of edges between 2 species</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="p">";</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="perl"></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;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$notableformat</span><span class="p">){</span><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">(</span><span class="si" style="color: #d14;">$i</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\t</span><span class="p">";}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">";}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="perl"><span class="p">}</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</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="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</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;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span> <span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$notableformat</span><span class="p">){</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">(</span><span class="si" style="color: #d14;">$i</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\t</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="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;">$j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">==</span><span class="nv" style="color: #008080;">$j</span><span class="p">){</span><span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]}</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="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="se" style="color: #d14;">\t</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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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="perl"> <span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><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="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 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="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="perl"><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">tput cols</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 class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">/=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></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="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="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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<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 class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">average number of edges</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</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="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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$sum</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$j</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;">$j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;">++</span><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;">$sum</span><span class="o" style="font-weight: 600;">+=</span><span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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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 class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$sum</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span></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;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="se" style="color: #d14;">\t</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="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="perl"> <span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="perl"><span class="nv" style="color: #008080;">$noheader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$last_isHeaderLine</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;">$isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="perl"><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">tput cols</span><span class="p">`;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="perl"><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># The 2-path matrix, the number of paths between 2 species of length 2</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="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="p">";</span></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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$notableformat</span><span class="p">){</span><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">(</span><span class="si" style="color: #d14;">$i</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\t</span><span class="p">";}</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">";}</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="perl"><span class="p">}</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="perl"><span class="nv" style="color: #008080;">$ret</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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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</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;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</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="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">(</span><span class="si" style="color: #d14;">$i</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\t</span><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;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$k</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;">$k</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$k</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="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]}</span><span class="o" style="font-weight: 600;">+=</span><span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$k</span><span class="p">]}</span><span class="o" style="font-weight: 600;">*</span><span class="nv" style="color: #008080;">$species_matrix</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$k</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="perl"> <span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]};</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="perl"> <span class="p">}</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]};</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</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;">$ret</span><span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret</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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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="perl"> <span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$ret</span><span class="p">);</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="perl"><span class="p">}</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="perl"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="perl"><span class="nv" style="color: #008080;">$noheader</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;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="nv" style="color: #008080;">$isHeaderLine</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;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="perl"><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">tput cols</span><span class="p">`;</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="perl"><span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">);</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">/=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">160</span><span class="p">;}</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="perl"></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="perl"><span class="nv" style="color: #008080;">processLine</span><span class="p">("</span><span class="s2" style="color: #d14;"># file</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">average number of 2-paths</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</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;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</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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237
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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;">$sum</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$j</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;">$j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</span><span class="p">;</span> <span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sum</span><span class="o" style="font-weight: 600;">+=</span><span class="nv" style="color: #008080;">$species_matrix_pow2</span><span class="p">{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]};</span></span>
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240
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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="LC241" class="line" lang="perl"> <span class="nv" style="color: #008080;">processLine</span><span class="p">(</span><span class="nv" style="color: #008080;">$keys</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">(</span><span class="si" style="color: #d14;">$i</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$sum</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@keys</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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<pre style="margin: 0;">+<span id="LC242" class="line" lang="perl"><span class="p">}</span></span>
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243
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244
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249
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250
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<pre style="margin: 0;">+<span id="LC251" 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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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="perl"> <span class="nv" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span><span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$notableformat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$_</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="perl"> </span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="perl"></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl</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;">$split_delim</span><span class="p">,</span><span class="nv" style="color: #008080;">$_</span><span class="p">);</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="perl"> </span>
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259
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<pre style="margin: 0;">+<span id="LC259" 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="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$_</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="perl"></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="perl"> <span class="nv" style="color: #008080;">@spl_backup</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@spl</span><span class="p">;</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="perl"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_header</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_header</span><span class="p">){</span><span class="nv" style="color: #008080;">$isHeaderLine</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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264
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<pre style="margin: 0;">+<span id="LC264" 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="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" 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;">$spl</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^# ?//g</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" 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;">@spl</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</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="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">){</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">=</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</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;">Corrected minimum table width: -w=</span><span class="si" style="color: #d14;">$maxNumOfCharsInOneLine</span><span class="s2" style="color: #d14;"> such that at least 1 character per column is displayed.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sumOfCharsLine</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">));</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="perl"></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isHeaderLine</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># is a header row </span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="nv" style="color: #008080;">$sumOfCharsLine</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># shave of chars from widest cell</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="perl"> <span class="nv" style="color: #008080;">$max_l</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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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="perl"> <span class="nv" style="color: #008080;">@max_l_is</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" 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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$max_l</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span><span class="nv" style="color: #008080;">$max_l</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">];</span><span class="nv" style="color: #008080;">@max_l_is</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@max_l_is</span><span class="p">,</span><span class="nv" style="color: #008080;">$i</span><span class="p">)}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$max_l</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@max_l_is</span><span class="p">,</span><span class="nv" style="color: #008080;">$i</span><span class="p">)}</span></span>
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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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="perl"> <span class="p">}</span></span>
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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">
277
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<pre style="margin: 0;">+<span id="LC277" 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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@max_l_is</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</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;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]],</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">...</span><span class="p">"</span> <span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</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;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]])</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="mi" style="color: #099;">1</span><span class="p">)</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>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl_backup</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$max_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]])</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="perl"> <span class="p">}</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="perl"> <span class="p">}</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sumOfCharsLine</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">));</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="perl"> <span class="p">}</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="perl"></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="perl"></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="nv" style="color: #008080;">$sumOfCharsLine</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># add of chars to smallest cell</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="perl"> <span class="nv" style="color: #008080;">$min_l</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$maxNumOfCharsInOneLine</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="perl"> <span class="nv" style="color: #008080;">@min_l_is</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" 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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$min_l</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span><span class="nv" style="color: #008080;">$min_l</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">];</span><span class="nv" style="color: #008080;">@min_l_is</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@min_l_is</span><span class="p">,</span><span class="nv" style="color: #008080;">$i</span><span class="p">)}</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="perl"> <span class="p">}</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" 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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@min_l_is</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="perl"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="perl"> <span class="nv" style="color: #008080;">$leftPad</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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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="perl"> <span class="nv" style="color: #008080;">$rightPad</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/( +)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$rightPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/^( +)/</span><span class="p">){</span><span class="nv" style="color: #008080;">$leftPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="perl"></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$leftPad</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$rightPad</span> <span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</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;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$min_l_is</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">";</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="perl"> <span class="p">}</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="perl"> </span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="perl"> <span class="p">}</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="perl"> <span class="nv" style="color: #008080;">$sumOfCharsLine</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nv" style="color: #008080;">@spl</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="p">}</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" 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="nv" style="color: #008080;">@spl_header</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@spl</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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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" 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;"># is not headerline -> do the same as in headerline</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="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl_header</span><span class="p">){</span><span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;}</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" 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;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@spl</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl_header</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span> <span class="c1" style="color: #998; font-style: italic;"># add pads</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="perl"> <span class="nv" style="color: #008080;">$leftPad</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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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="perl"> <span class="nv" style="color: #008080;">$rightPad</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/( +)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$rightPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/^( +)/</span><span class="p">){</span><span class="nv" style="color: #008080;">$leftPad</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$1</span><span class="p">}</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$leftPad</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$rightPad</span> <span class="p">){</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">];</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">";</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="perl"> <span class="p">}</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="perl"> <span class="p">}</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">></span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl_header</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]){</span> <span class="c1" style="color: #998; font-style: italic;"># trim</span></span>
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<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">],</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">...</span><span class="p">"</span> <span class="p">){</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">])</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">...</span><span class="p">"</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="perl"> <span class="p">}</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="perl"> <span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl_backup</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$spl</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">])</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="perl"> <span class="p">}</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isHeaderLine</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$last_isHeaderLine</span> <span class="p">){</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">|</span><span class="p">",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">);</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\|/+/g</span><span class="p">;</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^+]/-/g</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">|</span><span class="p">",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isHeaderLine</span> <span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">|</span><span class="p">",</span><span class="nv" style="color: #008080;">@spl</span><span class="p">);</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\|/+/g</span><span class="p">;</span><span class="nv" style="color: #008080;">$tmp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^+]/-/g</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp</span><span class="p">";}</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="perl"> <span class="nv" style="color: #008080;">$last_isHeaderLine</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$isHeaderLine</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="perl"> <span class="nv" style="color: #008080;">$isHeaderLine</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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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="perl"></span></pre>
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