From 6156a34ca04014d4fba17a5b42c47720e61f0163 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 15 Sep 2010 13:31:05 +0000
Subject: [PATCH] no_source_label_list to be called from mapper if it exists
only
---
.../xref_mapping/XrefMapper/DisplayXrefs.pm | 26 ++++++++++++-------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
index 9045b25d75..7510f6e5fd 100644
--- a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
@@ -802,7 +802,14 @@ GSQL
my $checked = 0;
my $added = 0;
my $removed = 0;
- my %no_source_name_in_desc = %{$self->no_source_label_list()};
+
+ my %no_source_name_in_desc;
+ if( $self->mapper->can("no_source_label_list") ){
+ foreach my $ext (@{$self->no_source_label_list()}){
+ $no_source_name_in_desc{$ext} = 1;
+ }
+ }
+
foreach my $gene_id (keys %genes_to_transcripts) {
@@ -1541,13 +1548,14 @@ sub check_desc{
}
-sub no_source_label_list{
- my $self = shift;
- my %list;
+#sub no_source_label_list{
+# my $self = shift;
+# my @list;
+
+## this needs to be added to the species .pm file
+## @list = qw(Uniprot/SWISSPROT Refseq_dna);
+##
+# return \@list;
+#}
-# foreach my $ex (qw(Uniprot/SWISSPROT Refseq_dna)){
-# $list{$ex} = 1;
-# }
- return \%list;
-}
1;
--
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