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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pftools">Debian Med / pftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/a5d923a3d3284c95a6ba13cf0fa6409fcad015db">a5d923a3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-17T15:35:16+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use upstream patch instead of own one
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#705310e1aeb0ce0575d7ee83f7af0d0988d1dc4e">
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+
debian/patches/0001-Harmonize-bin-env-path-Cleaning.patch
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</a>
</li>
<li class="file-stats">
<a href="#83da178741ee9770c8434f85e0d222f70d0d7713">
debian/patches/fix_perl_interpreter.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="705310e1aeb0ce0575d7ee83f7af0d0988d1dc4e">
<a href="https://salsa.debian.org/med-team/pftools/-/commit/a5d923a3d3284c95a6ba13cf0fa6409fcad015db#705310e1aeb0ce0575d7ee83f7af0d0988d1dc4e"><strong>debian/patches/0001-Harmonize-bin-env-path-Cleaning.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 342a8a5730c5b664741dff90a293f35818cb06d1 Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: smoretti <sebastien.moretti@sib.swiss></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Wed, 16 Dec 2020 18:08:06 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] Harmonize bin/env path + Cleaning</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> src/Perl/fasta_to_fastq.pl | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> src/Perl/make_iupac_cmp.pl | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> src/Perl/scramble_fasta.pl | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> src/Perl/sort_fasta.pl | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> tests/examples/test_V3.sh.cmake | 68 +++++++++----------</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> tests/examples/test_V3_output.sh.cmake | 3 -</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> tests/examples/test_pfsearchV3_iupac.pl.cmake | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> tests/examples/test_scan_search.pl.cmake | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> 8 files changed, 40 insertions(+), 43 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">--- a/src/Perl/fasta_to_fastq.pl</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/fasta_to_fastq.pl</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,3 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> #Copyright (c) 2010 LUQMAN HAKIM BIN ABDUL HADI (csilhah@nus.edu.sg)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/make_iupac_cmp.pl</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/make_iupac_cmp.pl</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env perl</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> use strict;</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> use Getopt::Std;</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/scramble_fasta.pl</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/scramble_fasta.pl</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env perl</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> use strict;</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/sort_fasta.pl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/sort_fasta.pl</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env perl</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> use strict;</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> use Getopt::Std;</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/examples/test_V3.sh.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/examples/test_V3.sh.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -19,9 +19,9 @@</span> PFW=$<TARGET_FILE:pfw></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> PTOH=$<TARGET_FILE:ptoh></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> PTOF=$<TARGET_FILE:ptof></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> P2FT=$<TARGET_FILE:2ft> # NB: sh does not allow variable name starting with a digit</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SORT_PSA=@PERL_SCRIPT_DIR@/sort_fasta.pl # FIXME: use cmake syntax </span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-MAKE_IUPAC_CMP=@PERL_SCRIPT_DIR@/make_iupac_cmp.pl # FIXME: use cmake syntax </span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SORT_PSA=@PERL_SCRIPT_DIR@/sort_fasta.pl # FIXME: use cmake syntax</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE_IUPAC_CMP=@PERL_SCRIPT_DIR@/make_iupac_cmp.pl # FIXME: use cmake syntax</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> SCRAMBLE=@PERL_SCRIPT_DIR@/scramble_fasta.pl # FIXME: use cmake syntax</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> CMPDIR=@DATA_DIR@/Matrices</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -29,15 +29,15 @@</span> TMPDIR=/tmp/test_V3</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> mkdir -p $TMPDIR</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# The PFTOOLS is a powerful software to align biological sequences. </span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Owing to the 'generalized profile syntax', it allows the fine-tuning </span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# of an alignent scoring system, beyond what is feasible by most other </span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# software. Despite the PFTOOLS are crippled by a lot of legacy code, </span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# they are still extremely useful for precision work . </span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# The PFTOOLS is a powerful software to align biological sequences.</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Owing to the 'generalized profile syntax', it allows the fine-tuning</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# of an alignent scoring system, beyond what is feasible by most other</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# software. Despite the PFTOOLS are crippled by a lot of legacy code,</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# they are still extremely useful for precision work.</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> # Nota bene to use this script as a testsuite:</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# (1) The output order of pfsearch is reproducible, as well as the one of </span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# pfsearchV3 with -t 1. </span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# (1) The output order of pfsearch is reproducible, as well as the one of</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# pfsearchV3 with -t 1.</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> # (2) Refrain using any pipe.</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -45,7 +45,7 @@</span> mkdir -p $TMPDIR</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> # Searching for the occurence of the SH3 domain within the VAV oncogene,</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> # using pfsearch V2 ...</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq </span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> # ...and using pfsearch V3:</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -53,8 +53,8 @@</span> $PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> $PFSEARCHV3 -n -t 1 -f ./sh3.prf ./VAV_HUMAN.seq</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Create a database of sequences and a database of profiles, each one </span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# with two entries. </span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Create a database of sequences and a database of profiles, each one</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# with two entries.</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> cat ./VAV_HUMAN.seq ./VAV_RAT.seq > $TMPDIR/VAV.seq</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> cat ./sh2.prf ./sh3.prf > $TMPDIR/SHX.prf</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="p">@@ -79,10 +79,10 @@</span> $PFSEARCHV3 -f -n -t 2 -o 6 ./sh3.prf -f</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> $PFSCANV3 -f -n -o 6 $TMPDIR/SHX.prf $TMPDIR/VAV.seq > $TMPDIR/SHX.pfscan3.hit</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# All these commands produces exactly the same list of matched </span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# sequences, with the same raw scores and coordinates. </span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# All these commands produces exactly the same list of matched</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# sequences, with the same raw scores and coordinates.</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# However the output order is not necessarily preserved here. </span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# However the output order is not necessarily preserved here.</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> # Let's verify that the output are comparable after fixing FASTA headers</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -95,7 +95,7 @@</span> diff $TMPDIR/SHX.pfscan2.out $TMPDIR/SHX</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> diff $TMPDIR/SHX.pfscan2.out $TMPDIR/SHX.pfsearch3.out # expecting no difference</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Pfsearch/pfscan V2 supports the following input formats for sequence: </span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Pfsearch/pfscan V2 supports the following input formats for sequence:</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> # FASTA, Swiss-Prot and EMBL.</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> $PFSEARCH -f ./sh3.prf ./VAV_HUMAN.seq # FASTA</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="p">@@ -105,10 +105,10 @@</span> $PFSEARCH ./sh3.prf ./GTPA_HUMAN.dat</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> $PFSCAN ./GTPA_HUMAN.dat ./sh3.prf # SwissProt</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> $PFSEARCH ./ecp.prf ./CVPBR322.embl # EMBL</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$PFSCAN ./CVPBR322.embl ./ecp.prf # EMBL </span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$PFSCAN ./CVPBR322.embl ./ecp.prf # EMBL</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Pfsearch/pfscan V3 supports the following input formats for sequence: </span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Pfsearch/pfscan V3 supports the following input formats for sequence:</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> # FASTA and FASTQ.</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> $PFSEARCHV3 -n -t 1 -f ./sh3.prf ./VAV_HUMAN.seq # FASTA</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="p">@@ -117,7 +117,7 @@</span> cat ./CVPBR322.embl \</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> | perl -ne 'if(/^ID +(\w+)/){print ">$1\n"}elsif(/^ /){s/[\s\d]+//g;print "$_\n";}' \</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> > $TMPDIR/CVPBR322.fa # Extract FASTA from EMBL</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> $PFSEARCHV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$PFSCANV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa </span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$PFSCANV3 -n -t 1 -f ./ecp.prf $TMPDIR/CVPBR322.fa</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> $PFSEARCHV3 -n -t 1 -q ./hiv.prf ./hiv.fastq # FASTQ</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> $PFSCANV3 -n -t 1 -q ./hiv.prf ./hiv.fastq # FASTQ</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="diff"><span class="p">@@ -136,8 +136,8 @@</span> $PFSEARCHV3 -n -fb ./ecp.prf $TMPDIR/CVP</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> diff -b $TMPDIR/ecp.CVPBR322.2.hit $TMPDIR/ecp.CVPBR322.3.hit # expecting no difference</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> </span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# The different PSA (i.e FASTA) output formats differ by the content </span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# their headers. The usage of XPSA (-o 6) is strongly recommended, the </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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# The different PSA (i.e FASTA) output formats differ by the content</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# their headers. The usage of XPSA (-o 6) is strongly recommended, the</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> # other formats being preserved for legacy.</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> $PFSEARCHV3 -n -f -o 1 -N 15 ./sh3.prf ./VAV_HUMAN.seq | $SORT_PSA -</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">
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="p">@@ -147,10 +147,10 @@</span> $PFSEARCHV3 -n -f -o 4 -N 15 ./sh3.prf .</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> $PFSEARCHV3 -n -f -o 6 -N 15 ./sh3.prf ./VAV_HUMAN.seq | $SORT_PSA - # recommended</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Multiple sequence alignment (MSA) can easily be produced from PSA </span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Multiple sequence alignment (MSA) can easily be produced from PSA</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> # using psa2msa (V2)</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$PFSEARCHV3 -n -f -o 6 ./ecp.prf $TMPDIR/CVPBR322.fa | $SORT_PSA - | $PSA2MSA </span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$PFSEARCHV3 -n -f -o 6 ./ecp.prf $TMPDIR/CVPBR322.fa | $SORT_PSA - | $PSA2MSA</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> # V3 has two new output formats: TSV and SAM</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -169,15 +169,15 @@</span> $PFSEARCHV3 -n -t 1 -q -o 8 ./hiv.prf</span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> $PFSEARCHV3 -n -t 1 -q -b -o 8 ./hiv.prf ./hiv.fastq # FASTQ to SAM</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Index can optionaly be used to speed-up database upload for pfsearch. </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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# This should be especially usefull for repetitive database searches </span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# using the heuristic. </span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Index can optionaly be used to speed-up database upload for pfsearch.</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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# This should be especially usefull for repetitive database searches</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# using the heuristic.</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> $PFINDEX -f -o $TMPDIR/CVPBR322.fa.idx $TMPDIR/CVPBR322.fa</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> $PFSEARCHV3 -n -f -o 7 ./ecp.prf $TMPDIR/CVPBR322.fa | sort > $TMPDIR/A.out # FASTA to TSV</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> $PFSEARCHV3 -n -f -i $TMPDIR/CVPBR322.fa.idx -o 7 ./ecp.prf $TMPDIR/CVPBR322.fa | sort > $TMPDIR/B.out # FASTA to TSV</span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-diff $TMPDIR/A.out $TMPDIR/B.out </span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+diff $TMPDIR/A.out $TMPDIR/B.out</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> </span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> $PFINDEX -q -o $TMPDIR/hiv.fastq.idx ./hiv.fastq</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> $PFSEARCHV3 -n -q -b -o 8 ./hiv.prf ./hiv.fastq | sort > $TMPDIR/A.out</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="p">@@ -185,23 +185,23 @@</span> $PFSEARCHV3 -n -q -b -o 8 -i $TMPDIR/hiv</span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> diff $TMPDIR/A.out $TMPDIR/B.out</span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Profile and/or sequence can be reversed on the fly. If both are </span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Profile and/or sequence can be reversed on the fly. If both are</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> # reversed the match score is the same</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> $PFSEARCHV3 -f -a rand_dna.prf rand_dna.seq</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> $PFSEARCHV3 -f -a -r -R rand_dna.prf rand_dna.seq</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# There is a much better support of rev/comp search in DNA sequences, </span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# There is a much better support of rev/comp search in DNA sequences,</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> # featuring the full IUPAC code.</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> # To illustrate these capabilities, let build a profile for bacterial</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# 16S sequence, starting from the Rfam seed RF00177.msa. First create </span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# 16S sequence, starting from the Rfam seed RF00177.msa. First create</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> # an adhoc substitution matrix</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> $MAKE_IUPAC_CMP -M 20 -m -30 > $TMPDIR/iupac20-30.cmp</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# ... let build a profile for bacterial 16S sequence, starting from </span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# ... let build a profile for bacterial 16S sequence, starting from</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> # the Rfam seed RF00177.msa.</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> cat ./RF00177.msa \</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="p">@@ -224,7 +224,7 @@</span> cat ./SRR9619541.sample.fastq \</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> > $TMPDIR/permut.fa</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> # $PFCALIBRATEV3 -F $TMPDIR/permut.fa $TMPDIR/16S.prf.tmp > $TMPDIR/16S.prf</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# $PFSEARCHV3 -t 1 -n -q $TMPDIR/16S.prf $TMPDIR/small.sample.fastq </span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# $PFSEARCHV3 -t 1 -n -q $TMPDIR/16S.prf $TMPDIR/small.sample.fastq</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> #----------------------------------------------------------------------#</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> # Verify handling of characters not in the profile alphabet</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="p">@@ -240,7 +240,7 @@</span> ACGTWACGT</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> EOI</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> $PFMAKE -m -3 -S 0.01 -F 100 $TMPDIR/ACGTAACGT.seq $CMPDIR/dna_50_40.cmp > $TMPDIR/ACGTAACGT.prf</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTAACGT.seq # raw_score=450 PSA=ACGTAACGT </span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTAACGT.seq # raw_score=450 PSA=ACGTAACGT</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> $PFSEARCHV3 -fa -o 6 $TMPDIR/ACGTAACGT.prf $TMPDIR/ACGTWACGT.seq # raw_score=383 PSA=ACGTWACGT (not ACGTXACGT)</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/examples/test_V3_output.sh.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/examples/test_V3_output.sh.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="p">@@ -13,6 +13,3 @@</span> mkdir -p $TMPDIR</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> sh -ve ./test_V3.sh > $TMPDIR/test_V3.out 2>/dev/null</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> diff ./test_V3.out $TMPDIR/test_V3.out</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/examples/test_pfsearchV3_iupac.pl.cmake</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/examples/test_pfsearchV3_iupac.pl.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> use strict;</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/examples/test_scan_search.pl.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/examples/test_scan_search.pl.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> use strict;</span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> </span></pre>
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<br>
</li>
<li id="83da178741ee9770c8434f85e0d222f70d0d7713">
<a href="https://salsa.debian.org/med-team/pftools/-/commit/a5d923a3d3284c95a6ba13cf0fa6409fcad015db#83da178741ee9770c8434f85e0d222f70d0d7713"><strong>debian/patches/fix_perl_interpreter.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(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">@@ -10,3 +10,11 @@ Description: Fix interpreter of perl script to fix build time test</td>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> use strict;</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> use Getopt::Std;</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/make_iupac_cmp.pl</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/make_iupac_cmp.pl</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> use strict;</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> use Getopt::Std;</span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/commit/a5d923a3d3284c95a6ba13cf0fa6409fcad015db#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">spelling.patch</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">fix_perl_interpreter.patch</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># fix_perl_interpreter.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">0001-Harmonize-bin-env-path-Cleaning.patch</span></pre>
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