From a5d38a9b2fdc771e66b1ab1d1773573e01414059 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Tue, 13 Jan 2004 12:09:01 +0000
Subject: [PATCH] return empty list instead of throwing in
get_all_translateable_Exons when there is no Translation
---
modules/Bio/EnsEMBL/Transcript.pm | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 2b44576cb5..21df29edc4 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -350,7 +350,7 @@ sub translation {
} elsif( !exists $self->{'translation'} and defined $self->adaptor() ) {
$self->{'translation'} =
$self->adaptor()->db()->get_TranslationAdaptor()->
- fetch_by_Transcript( $self );
+ fetch_by_Transcript( $self );
}
return $self->{'translation'};
}
@@ -1103,7 +1103,7 @@ sub three_prime_utr {
Description: Returns a list of exons that translate with the
start and end exons truncated to the CDS regions.
Returntype : listref Bio::EnsEMBL::Exon
- Exceptions : If there is no Translation object
+ Exceptions : throw if translation has invalid information
Caller : Genebuild, $self->translate()
=cut
@@ -1112,8 +1112,8 @@ sub three_prime_utr {
sub get_all_translateable_Exons {
my ( $self ) = @_;
- my $translation = $self->translation
- or throw("No translation attached to transcript object");
+ #return an empty list if there is no translation (i.e. pseudogene)
+ my $translation = $self->translation or return [];
my $start_exon = $translation->start_Exon;
my $end_exon = $translation->end_Exon;
my $t_start = $translation->start;
--
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