From 32e63746dcd76c1207133639f26c66c22586447e Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 17 May 2011 13:09:57 +0000
Subject: [PATCH] do not remove MGI: from the stat only remove ZFIN_ID: and
HGNC:. MGI number is stored with the MGI:
---
.../xref_mapping/XrefParser/VegaOfficialNameParser.pm | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
index 72de13255e..843cddf0a8 100644
--- a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
@@ -24,6 +24,7 @@ sub run_script {
my $species_name = $id2name{$species_id}[0];
my $source_name;
+ my $prepend = 1;
if($my_args =~ /source[=][>](\S+?)[,]/){
$source_name = $1;
}
@@ -34,6 +35,7 @@ sub run_script {
}
elsif($species_name eq "mus_musculus" ){
$source_name = "MGI";
+ $prepend = 0;
$host = "ens-staging2";
}
elsif($species_name eq "danio_rerio" ){
@@ -256,8 +258,10 @@ EXT
if(defined($ext_to_core{$key} )){
my $ext = $vega_to_ext{$key};
- my $regex = $source_name . ':';
- $ext =~ s/$regex//;
+ if($prepend){
+ my $regex = $source_name . ':';
+ $ext =~ s/$regex//;
+ }
my $stable_id = $ext_to_core{$key};
if(!defined($label{$ext})){
--
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