From e36a69857536a6c833abf322616d8370428fe84e Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 25 Jul 2011 17:00:34 +0000
Subject: [PATCH] Get descriptions from _mRNA and _ncRNA
---
.../XrefParser/RefSeq_CCDSParser.pm | 19 +++++++++++--------
1 file changed, 11 insertions(+), 8 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
index d90496a256..c06bbf3b6a 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
@@ -53,15 +53,18 @@ sub run_script {
my %description;
my $dbi = $self->dbi();
- my $sql = "select xref.accession, xref.label, xref.version, xref.description from xref, source where xref.source_id = source.source_id and source.name like 'RefSeq_%RNA'";
+
+ my $sql = "select xref.accession, xref.label, xref.version, xref.description from xref, source where xref.source_id = source.source_id and source.name = ?";
my $sth = $dbi->prepare($sql);
- $sth->execute();
- my ($acc, $lab, $ver, $desc);
- $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
- while (my @row = $sth->fetchrow_array()) {
- $label{$acc} = $lab;
- $version{$acc} = $ver;
- $description{$acc} = $desc;
+ foreach my $refseq (qw(RefSeq_mRNA RefSeq_ncRNA)){
+ $sth->execute($refseq);
+ my ($acc, $lab, $ver, $desc);
+ $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
+ while (my @row = $sth->fetchrow_array()) {
+ $label{$acc} = $lab;
+ $version{$acc} = $ver;
+ $description{$acc} = $desc;
+ }
}
$sth->finish;
--
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