From 5c4fad5f3b473424ccb98756442682247ab11b8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 1 Sep 2009 13:34:52 +0000
Subject: [PATCH] Patch from Dan Staines to sorting of seq-edits.
---
modules/Bio/EnsEMBL/Translation.pm | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index 9b9a44e17a..03bd172624 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -955,18 +955,20 @@ sub get_all_SeqEdits {
=cut
sub modify_translation {
- my ($self, $seq) = @_;
+ my ( $self, $seq ) = @_;
- my @seqeds = @{$self->get_all_SeqEdits()};
+ my @seqeds = @{ $self->get_all_SeqEdits() };
- # sort in reverse order to avoid complication of adjusting downstream edits
- @seqeds = sort {$b <=> $a} @seqeds;
+ # Sort in reverse order to avoid complication of adjusting
+ # downstream edits.
+ @seqeds = sort { $b->start() <=> $a->start() } @seqeds;
- # apply all edits
+ # Apply all edits.
my $peptide = $seq->seq();
foreach my $se (@seqeds) {
- $se->apply_edit(\$peptide);
+ $se->apply_edit( \$peptide );
}
+
$seq->seq($peptide);
return $seq;
--
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