From a2c015650bb4c9762703d26a5f7be75f7b92c018 Mon Sep 17 00:00:00 2001
From: William McLaren <wm2@ebi.ac.uk>
Date: Fri, 13 Aug 2010 08:48:36 +0000
Subject: [PATCH] Fix for splice sites being called at transcript ends
---
modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
index 8c3946d40f..1a5c0f8490 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
@@ -459,14 +459,26 @@ sub type_variation {
if ($splice_site_2 or $splice_site_3) {
+ my ($se_s, $se_e, $ee_s, $ee_e) = ($tr->start_Exon->start, $tr->start_Exon->end, $tr->end_Exon->start, $tr->end_Exon->end);
+ ($se_s, $se_e, $ee_s, $ee_e) = ($se_e, $se_s, $ee_e, $ee_s) if $tr->strand < 0;
+
# check coord relative to first exon
# near beginning of first exon is obv not a splice site
- if($var->start < $tr->start_Exon->end) {
- if($tr->start_Exon->end - $var->start <= 3) {
+ if($var->start <= $se_e) {
+ if(abs($se_e - $var->start) <= 3) {
+ $var->type('SPLICE_SITE');
+ }
+ }
+
+ # also check relative to last exon
+ # near end of last exon is also not a splice site
+ elsif($var->start >= $ee_s) {
+ if(abs($ee_s - $var->start) <= 3) {
$var->type('SPLICE_SITE');
}
}
+ # if not near either end of transcript, then it is definitely a splice site
else {
$var->type('SPLICE_SITE');
}
--
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