From c8e4ebe3d5bd3d946fe4968315ff2987e9002008 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 13 Sep 2016 09:43:54 +0100
Subject: [PATCH] ENSCORESW-1894: deal with stop codons across exons
---
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm | 24 +++++++++----------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
index 26370e1d69..ed776deda8 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
@@ -319,18 +319,18 @@ sub print_feature {
my $exon_start = $cdsexon->start;
my $exon_end = $cdsexon->end;
- if ( $translation &&
- $hasend &&
- ( $exon->end >= $endcodons[0]->start &&
- $exon->start <= $endcodons[0]->end ) )
- {
- # Only the first stop-codon feature is used to adjust the end of the exon
- # This may not be sufficient all the time
- if ( $cdsexon->strand == 1 ) {
- $exon_end = $cdsexon->end - $endcodons[0]->length;
- }
- else {
- $exon_start = $cdsexon->start + $endcodons[0]->length;
+ foreach my $endcodon (@endcodons) {
+ if ( $translation &&
+ $hasend &&
+ ( $exon->end >= $endcodon->start &&
+ $exon->start <= $endcodon->end ) )
+ {
+ if ( $cdsexon->strand == 1 ) {
+ $exon_end = $cdsexon->end - $endcodon->length;
+ }
+ else {
+ $exon_start = $cdsexon->start + $endcodon->length;
+ }
}
}
--
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