From 4d89cbc7d622b9f36e7a4af3690a383330f24c27 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 28 Jul 2004 10:07:17 +0000
Subject: [PATCH] allow alternate codon tables to be used for translations
---
modules/Bio/EnsEMBL/Transcript.pm | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 7c0c26a9d2..5284770f2e 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1188,7 +1188,7 @@ sub translate {
# remove final stop codon from the mrna if it is present
# produced peptides will not have '*' at end
- # if terminal stop codon is desired call translatable_seq directly
+ # if terminal stop codon is desired call translatable_seq directly
# and produce a translation from it
if( CORE::length( $mrna ) % 3 == 0 ) {
@@ -1200,7 +1200,19 @@ sub translate {
-alphabet => 'dna',
-id => $display_id );
- my $translation = $peptide->translate();
+ # Alternative codon tables (such as the mitochondrial codon table) can
+ # be sepcified for a sequence region via the seq_region_attrib table.
+ # A list of codon tables and their codes is at:
+ # http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
+
+ my $codon_table;
+ if($self->slice()) {
+ ($codon_table) = @{$self->slice()->get_all_Attributes('codon_table')};
+ }
+
+ $codon_table ||= 1; # default vertebrate codon table
+
+ my $translation = $peptide->translate(undef,undef,undef,$codon_table);
if($self->edits_enabled()) {
$self->translation()->modify_translation( $translation );
--
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