From b61e8e624e01c799e330be05716ccde47b7a8429 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 23 Dec 2014 08:02:04 +0000
Subject: [PATCH] ENSCORESW-1191: regex updated to catch Name and Synonyms
across multiple lines, with possible evidence codes
---
.../xref_mapping/XrefParser/UniProtParser.pm | 26 ++++++++++---------
1 file changed, 14 insertions(+), 12 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index e19825cd98..6cd96ca187 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -372,20 +372,20 @@ sub create_xrefs {
#print "Adding " . $xref->{ACCESSION} . " " . $xref->{LABEL} ."\n";
- my ($gns) = $_ =~ /(GN\s+Name.+)/; # /s allows . to match newline
+ my ($gns) = $_ =~ /(GN\s+.+)/s;
my @gn_lines = ();
- if ( defined $gns ) { @gn_lines = split /\n/, $gns }
+ if ( defined $gns ) { @gn_lines = split /;/, $gns }
# Do not allow the addition of UniProt Gene Name dependent Xrefs
# if the protein was imported from Ensembl. Otherwise we will
# re-import previously set symbols
if(! $ensembl_derived_protein) {
+ my %depe;
foreach my $gn (@gn_lines){
my $gene_name = undef;
- my %depe;
- if($gn =~ /Name=((.*?))[;\s]/){
- $depe{LABEL} = uc($1);
+ if($gn =~ /Name=((.*?))[;\s]/s){ # /s for multi-line entries ; is the delimiter
+ $depe{LABEL} = $1; # leave name as is, upper/lower case is relevant in gene names
$depe{ACCESSION} = $self->get_name($xref->{ACCESSION},$depe{LABEL});
$gene_name = $depe{ACCESSION};
@@ -394,13 +394,15 @@ sub create_xrefs {
$depe{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
push @{$xref->{DEPENDENT_XREFS}}, \%depe;
$dependent_xrefs{"Uniprot_gn"}++;
- my @syn;
- if($gn =~ /Synonyms=([^;]+);/){
- my $syn = $1;
- $syn =~ s/\s+//g;
- @syn= split(/,/,$syn);
- push (@{$depe{"SYNONYMS"}}, @syn);
- }
+ }
+ my @syn;
+ if($gn =~ /Synonyms=(.*)/s){ # use of /s as synonyms can be across more than one line
+ my $syn = $1;
+ $syn =~ s/{.*}//g;
+ $syn =~ s/\n//g;
+ $syn =~ s/\s+//g;
+ @syn = split(/,/,$syn);
+ push (@{$depe{"SYNONYMS"}}, @syn);
}
}
}
--
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