From eab2a5ccd524e8895c38c35695d8aedc90bd0684 Mon Sep 17 00:00:00 2001
From: Ewan Birney <birney@sanger.ac.uk>
Date: Thu, 21 Feb 2002 15:48:45 +0000
Subject: [PATCH] fixes when arne was looking over my shoulder!!
---
modules/Bio/EnsEMBL/Transcript.pm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 967b23c01d..bde9cdb2c4 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1214,7 +1214,7 @@ sub convert_peptide_coordinate_to_contig {
# move start end into translate cDNA coordinates now.
# much easier!
- $start = 3* $start;
+ $start = 3* $start-2;
$end = 3* $end;
if( !defined $self->translation ) {
@@ -1241,7 +1241,7 @@ sub convert_peptide_coordinate_to_contig {
my $exon;
while( $exon = shift @exons && $start < $trans_len + $current_len_exon ) {
- ;
+ $trans_len += $exon->length();
}
unshift(@exons,$exon);
@@ -1263,7 +1263,7 @@ sub convert_peptide_coordinate_to_contig {
} else {
$end_in_exon = $exon->length;
}
-
+ $offset_into_exon = 0;
# the main reason for make this an attribute of the exon is to handle stickies
push(@out,$exon->contig_seqfeatures_from_relative_position($start_in_exon,$end_in_exon));
--
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