From 6dbed007a6663728aaf3c47a65268ade92f6cfa2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 13 Aug 2010 13:45:26 +0000
Subject: [PATCH] Modified previous bugfix in seq(): If stable IDs are not
available, and dbIDs are not available, use genomic start/end coordinates to
figure out whether "this" translation is the same as the canonical
translation or not.
---
modules/Bio/EnsEMBL/Translation.pm | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index ee11346f58..32b3738418 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -853,11 +853,21 @@ sub seq {
if ( defined( $canonical_translation->stable_id() )
&& defined( $self->stable_id() ) )
{
+ # Try stable ID.
$is_alternative =
( $canonical_translation->stable_id() ne $self->stable_id() );
- } else {
+ } elsif ( defined( $canonical_translation->dbID() )
+ && defined( $self->dbID() ) )
+ {
+ # Try dbID.
$is_alternative =
( $canonical_translation->dbID() != $self->dbID() );
+ } else {
+ # Resort to using geomic start/end coordinates.
+ $is_alternative = ( ($canonical_translation->genomic_start() !=
+ $self->genomic_start() )
+ || ( $canonical_translation->genomic_end() !=
+ $self->genomic_end() ) );
}
if ($is_alternative) {
--
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