From 681a74a9a5048d4fa574cb1cabe1a8f538cecfec Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 6 Sep 2012 14:43:00 +0000
Subject: [PATCH] no need to use a hash of the species name when the species
name is hard-coded
---
.../XrefParser/VegaOfficialNameParser.pm | 15 ++++-----------
1 file changed, 4 insertions(+), 11 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
index 1e659ff981..7c8fd36443 100644
--- a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
@@ -101,13 +101,6 @@ sub run_script {
$cpass = $1;
}
-#populate species hash - source name is the hash key
- my %species_names = (
- HGNC => "human",
- ZFIN_ID => "zebrafish",
- MGI => "mouse"
- );
-
my $vega_dbc;
my $core_dbc;
@@ -142,15 +135,15 @@ sub run_script {
-host => $host,
-user => $user);
- $vega_dbc = $reg->get_adaptor($species_names{$source_name},"vega","slice");
+ $vega_dbc = $reg->get_adaptor($species_name,"vega","slice");
if(!defined($vega_dbc)){
- print "Could not connect to $species_names{$source_name} vega database using load_registry_from_db $host $user\n";
+ print "Could not connect to $species_name vega database using load_registry_from_db $host $user\n";
return 1;
}
$vega_dbc = $vega_dbc->dbc;
- $core_dbc = $reg->get_adaptor($species_names{$source_name},"core","slice");
+ $core_dbc = $reg->get_adaptor($species_name,"core","slice");
if(!defined($core_dbc)){
- print "Could not connect to $species_names{$source_name} core database using load_registry_from_db $host $user\n";
+ print "Could not connect to $species_name core database using load_registry_from_db $host $user\n";
return 1;
}
$core_dbc= $core_dbc->dbc;
--
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