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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bioperl">Debian Med / bioperl</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bioperl/-/commit/3ac0f27124dfc37fd2bd4b1c0165a2bf64dd1ede">3ac0f271</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-10-28T20:41:40+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Introduced patch to parse old and new FT lines
The specification of isoforms is not yet supported.
</pre>
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<h4>2 changed files:</h4>
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<a href="#782d0150501d7b426c6675859bd549776ab8c5ba">
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+
debian/patches/FTlineParsingHickups.patch
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+
debian/patches/series
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<h4>Changes:</h4>
<li id="782d0150501d7b426c6675859bd549776ab8c5ba">
<a href="https://salsa.debian.org/med-team/bioperl/-/commit/3ac0f27124dfc37fd2bd4b1c0165a2bf64dd1ede#782d0150501d7b426c6675859bd549776ab8c5ba"><strong>debian/patches/FTlineParsingHickups.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Title: Fix parsing of new UniProt FT lines</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">URL: https://github.com/bioperl/bioperl-live/pull/348</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bioperl/lib/Bio/SeqIO/swiss.pm</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl.orig/lib/Bio/SeqIO/swiss.pm</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl/lib/Bio/SeqIO/swiss.pm</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1289,7 +1289,7 @@</span> sub _read_FTHelper_swissprot {</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> $desc, # The descriptive text</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> $ftid, # feature Id is like a qualifier but there can be only one of them</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> );</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)\s*(.*)$/ox) {</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)[\s.]+([\d\?\>]+)\s*(.*)$/ox) {</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> $key = $1;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> my $loc1 = $2;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> my $loc2 = $3;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -1300,9 +1300,20 @@</span> sub _read_FTHelper_swissprot {</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> $desc = "";</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } elsif ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+(.*)$/ox) {</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $key = $1;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $loc1 = $2;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $loc2 = $2;</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;">+ $loc = "$loc1";</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ($3 && (length($3) > 0)) {</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $desc = $3;</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chomp($desc);</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } else {</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $desc = "";</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- while ( defined($_ = $self->_readline) && /^FT\s{20,}(\S.*)$/ ) {</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while ( defined($_ = $self->_readline) && /^FT\s{4,}(\S.*)$/ ) {</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> my $continuation_line = $1;</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> if ( $continuation_line =~ /.FTId=(.*)\./ ) {</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> $ftid=$1;</span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl/-/commit/3ac0f27124dfc37fd2bd4b1c0165a2bf64dd1ede#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">FTlineParsingHickups.patch</span></pre>
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