From 08998c862d664f747ef7b71a140c8707e272ff82 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 4 Apr 2012 08:44:32 +0000
Subject: [PATCH] changes to accommodate multiple ensembl stable ids linking to
the same vega stable id
---
.../XrefParser/curated_transcriptParser.pm | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
index c3600ca957..c9fbe1d04f 100644
--- a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
@@ -162,7 +162,7 @@ sub run_script {
my %ott_to_vega_name;
- my %ott_to_enst;
+ my %enst_to_ott;
my $sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";
@@ -170,11 +170,11 @@ sub run_script {
foreach my $external_db (qw(Vega_transcript shares_CDS_with_OTTT shares_CDS_and_UTR_with_OTTT OTTT)){
$sth->execute($external_db) or croak( $core_dbc->errstr());
while ( my @row = $sth->fetchrow_array() ) {
- $ott_to_enst{$row[1]} = $row[0];
+ $enst_to_ott{$row[0]} = $row[1];
}
}
- print "We have ".scalar(%ott_to_enst)." ott to enst entries\n " if($verbose);
+ print "We have ".scalar(keys %enst_to_ott)." ott to enst entries\n " if($verbose);
my $dbi = $self->dbi();
@@ -193,7 +193,8 @@ sub run_script {
my $xref_count = 0;
- foreach my $ott (keys %ott_to_enst){
+ foreach my $enst (keys %enst_to_ott){
+ my $ott = $enst_to_ott{$enst};
if(defined($ott_to_vega_name{$ott})){
my $id = $curated_source_id;
my $name = $ott_to_vega_name{$ott};
@@ -210,10 +211,10 @@ sub run_script {
info_type => "DIRECT"} );
$xref_count++;
- $self->add_direct_xref($xref_id, $ott_to_enst{$ott}, "transcript", "");
+ $self->add_direct_xref($xref_id, $enst, "transcript", "");
}
if(defined($ott_to_status{$ott})){
- $status_insert_sth->execute($ott_to_enst{$ott}, $ott_to_status{$ott});
+ $status_insert_sth->execute($enst, $ott_to_status{$ott});
}
}
--
GitLab