From e88eb3bd771ef3431cf392529596b80d6f92cc2c Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 12 Jan 2012 23:43:44 +0000
Subject: [PATCH] Bugfix for issue raised by Michael Nuhn from Ensembl Genomes.
fetch_all_by_Transcript_list() incorrectly assigned the canonical translation
ID
---
modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index ba603fe3f8..8bb1b27887 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -745,7 +745,7 @@ sub fetch_all_by_Transcript_list {
# splitting large queries into smaller queries of 200 ids
my $max_size = 200;
- my ( $tr_id,$tl_id, $start_exon_id, $end_exon_id,
+ my ( $transcript_id, $translation_id, $start_exon_id, $end_exon_id,
$seq_start, $seq_end, $stable_id, $version,
$created_date, $modified_date );
@@ -765,6 +765,10 @@ sub fetch_all_by_Transcript_list {
} else {
$id_str = " = " . $ids[0];
}
+
+ my $canonical_lookup = $self->dbc()->sql_helper()->execute_into_hash(
+ -SQL => 'SELECT transcript_id, canonical_translation_id FROM transcript WHERE transcript_id '.$id_str
+ );
my $created_date = $self->db->dbc->from_date_to_seconds("tl.created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("tl.modified_date");
@@ -779,7 +783,7 @@ sub fetch_all_by_Transcript_list {
$sth->execute();
- $sth->bind_columns( \$tr_id, \$tl_id, \$start_exon_id, \$end_exon_id,
+ $sth->bind_columns( \$transcript_id, \$translation_id, \$start_exon_id, \$end_exon_id,
\$seq_start, \$seq_end, \$stable_id, \$version,
\$created_date, \$modified_date );
@@ -789,7 +793,7 @@ sub fetch_all_by_Transcript_list {
# this will load all the exons whenever we load the translation
# but I guess thats ok ....
- my $tr = $trans_hash{$tr_id};
+ my $tr = $trans_hash{$transcript_id};
foreach my $exon (@{$tr->get_all_Exons()}) {
if(!$start_exon && $exon->dbID() == $start_exon_id ) {
@@ -808,7 +812,7 @@ sub fetch_all_by_Transcript_list {
}
my $tl = Bio::EnsEMBL::Translation->new
- (-dbID => $tl_id,
+ (-dbID => $translation_id,
-seq_start => $seq_start,
-seq_end => $seq_end,
-start_exon => $start_exon,
@@ -819,7 +823,8 @@ sub fetch_all_by_Transcript_list {
-modified_date => $modified_date || undef);
$tl->adaptor($self);
- $tr->translation($tl);
+ my $canonical_translation_id = $canonical_lookup->{$transcript_id};
+ $tr->translation($tl) if $translation_id == $canonical_translation_id;
push @out, $tl;
}
--
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