From 81f06bd0764533ad0cfa1ee58279709d18da6af8 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 09:17:31 +0000
Subject: [PATCH] If the translations do not have stable IDs, use their dbIDs
to compare them instead. Bug fix for Amy.
---
modules/Bio/EnsEMBL/Translation.pm | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index 61ccaeccd3..ee11346f58 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -848,8 +848,17 @@ sub seq {
my $transcript = $self->transcript();
my $canonical_translation = $transcript->translation();
- my $is_alternative =
- ( $canonical_translation->stable_id() ne $self->stable_id() );
+ my $is_alternative;
+
+ if ( defined( $canonical_translation->stable_id() )
+ && defined( $self->stable_id() ) )
+ {
+ $is_alternative =
+ ( $canonical_translation->stable_id() ne $self->stable_id() );
+ } else {
+ $is_alternative =
+ ( $canonical_translation->dbID() != $self->dbID() );
+ }
if ($is_alternative) {
# To deal with non-canonical (alternative) translations, subsitute
--
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