From 6ff0e047db13214b2b61015d02fda507e8ceeffe Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 29 Sep 2008 16:33:14 +0000
Subject: [PATCH] use external db display name rather than dbname for source in
descriptions
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 9cb8945b73..07aa90b753 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -3379,18 +3379,18 @@ sub new_build_gene_descriptions{
my %external_name_to_id;
my %ex_db_id_to_status;
- my %ex_db_id_to_name;
- my $sql1 = "SELECT external_db_id, db_name, status from external_db";
+ my %ex_db_id_to_display_name;
+ my $sql1 = "SELECT external_db_id, db_name, status, db_display_name from external_db";
my $sth1 = $self->core->dbc->prepare($sql1)
|| die "prepare failed for $sql1\n";
$sth1->execute() || die "execute failed";
- my ($db_id, $name, $status);
- $sth1->bind_columns(\$db_id, \$name, \$status);
+ my ($db_id, $name, $status, $display_name);
+ $sth1->bind_columns(\$db_id, \$name, \$status, \$display_name);
while($sth1->fetch()){
$external_name_to_id{$name} = $db_id;
$ex_db_id_to_status{$db_id} = $status;
- $ex_db_id_to_name{$db_id} = $name;
+ $ex_db_id_to_display_name{$db_id} = $display_name;
}
$sth1->finish;
@@ -3639,7 +3639,7 @@ GSQL
$description =~ s/\"//ig; # remove " as they will cause problems in .sql files
- my $desc = $description . " [Source:".$ex_db_id_to_name{$ex_db{$best_gene_xref}}.";Acc:$acc]";
+ my $desc = $description . " [Source:".$ex_db_id_to_display_name{$ex_db{$best_gene_xref}}.";Acc:$acc]";
print GENE_DESCRIPTIONS "UPDATE gene g SET g.description=\"$desc\" ".
"WHERE g.gene_id=$gene_id;\n" if ($description);
--
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