From b49ec44c9d7962d7228b8251f5608db048a94c72 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 13 Jul 2011 08:40:10 +0000
Subject: [PATCH] changed the setting of the accession for unigene to call a
subroutine so that this can be overwritten in an alternative version to be
used here but ensembl genomes to use the original still
---
.../xref_mapping/XrefParser/UniProtParser.pm | 23 +++++++------------
1 file changed, 8 insertions(+), 15 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index a7fc90a45a..2d82b3c578 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -408,7 +408,7 @@ sub create_xrefs {
if($gn =~ /Name=(\S+);/){
$depe{LABEL} = uc($1);
- $depe{ACCESSION} = $xref->{ACCESSION};
+ $depe{ACCESSION} = $self->get_name($xref->{ACCESSION},$depe{LABEL});
$gene_name = $depe{ACCESSION};
$depe{SOURCE_NAME} = "Uniprot_genename";
@@ -573,20 +573,6 @@ sub create_xrefs {
print "Found $num_sp_pred predicted SwissProt xrefs and $num_sptr_pred predicted SPTrEMBL xrefs\n" if (($num_sp_pred > 0 || $num_sptr_pred > 0) and $verbose);
-# my $kount=0;
- my $genename_source_id = $dependent_sources{"Uniprot_genename"};
- foreach my $namekey (keys %GeneNameSynonym){
- #add xref
- my $xref_id = $self->add_xref($namekey,"",$namekey, "", $genename_source_id, $species_id,"DEPENDENT");
-# $kount++;
-# print $namekey."\t";
- foreach my $synkey (keys %{$GeneNameSynonym{$namekey}}){
- #add synonyms for xref
- $self->add_synonym($xref_id, $synkey);
-# print "$synkey, ";
- }
-# print "\n";
- }
# print "$kount gene anmes added\n";
@@ -602,4 +588,11 @@ sub create_xrefs {
#TODO - currently include records from other species - filter on OX line??
}
+sub get_name {
+ my $self = shift;
+ my $acc = shift;
+ my $label = shift;
+
+ return $acc;
+}
1;
--
GitLab