[med-svn] [Git][med-team/bioperl][master] Introduced patch to parse old and new FT lines

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bioperl


Commits:
3ac0f271 by Steffen Moeller at 2020-10-28T20:41:40+01:00
Introduced patch to parse old and new FT lines

The specification of isoforms is not yet supported.

- - - - -


2 changed files:

- + debian/patches/FTlineParsingHickups.patch
- + debian/patches/series


Changes:

=====================================
debian/patches/FTlineParsingHickups.patch
=====================================
@@ -0,0 +1,38 @@
+Author: Steffen Moeller <moeller at debian.org>
+Title: Fix parsing of new UniProt FT lines
+URL: https://github.com/bioperl/bioperl-live/pull/348
+Index: bioperl/lib/Bio/SeqIO/swiss.pm
+===================================================================
+--- bioperl.orig/lib/Bio/SeqIO/swiss.pm
++++ bioperl/lib/Bio/SeqIO/swiss.pm
+@@ -1289,7 +1289,7 @@ sub _read_FTHelper_swissprot {
+         $desc,                  # The descriptive text
+         $ftid,                  # feature Id is like a qualifier but there can be only one of them
+        );
+-    if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)\s*(.*)$/ox) {
++    if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)[\s.]+([\d\?\>]+)\s*(.*)$/ox) {
+         $key = $1;
+         my $loc1 = $2;
+         my $loc2 = $3;
+@@ -1300,9 +1300,20 @@ sub _read_FTHelper_swissprot {
+         } else {
+             $desc = "";
+         }
++    } elsif ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+(.*)$/ox) {
++        $key = $1;
++        my $loc1 = $2;
++        my $loc2 = $2;
++        $loc = "$loc1";
++        if ($3 && (length($3) > 0)) {
++            $desc = $3;
++            chomp($desc);
++        } else {
++            $desc = "";
++        }
+     }
+ 
+-    while ( defined($_ = $self->_readline) && /^FT\s{20,}(\S.*)$/ ) {
++    while ( defined($_ = $self->_readline) && /^FT\s{4,}(\S.*)$/ ) {
+         my $continuation_line = $1;
+         if ( $continuation_line =~ /.FTId=(.*)\./ ) {
+             $ftid=$1;


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+FTlineParsingHickups.patch



View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/commit/3ac0f27124dfc37fd2bd4b1c0165a2bf64dd1ede

-- 
View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/commit/3ac0f27124dfc37fd2bd4b1c0165a2bf64dd1ede
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