From bbeb1814805e9e3c756a2f93b41b2b0f281172d0 Mon Sep 17 00:00:00 2001
From: Yuan Chen <yuan@sanger.ac.uk>
Date: Mon, 10 Oct 2005 10:21:03 +0000
Subject: [PATCH] check strand for REGULATORY_REGION as well
---
.../Bio/EnsEMBL/Utils/TranscriptAlleles.pm | 19 +++++++++++--------
1 file changed, 11 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
index bb74845580..91ab625ff2 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
@@ -42,11 +42,12 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Variation::ConsequenceType;
use vars qw(@ISA @EXPORT_OK);
+use Data::Dumper;
+
@ISA = qw(Exporter);
@EXPORT_OK = qw(get_all_ConsequenceType type_variation);
-use Data::Dumper;
=head2 get_all_ConsequenceType
@@ -75,7 +76,7 @@ sub get_all_ConsequenceType {
throw('Bio::EnsEMBL::Transcript argument is required.');
}
- if(!ref($alleles) || (ref($alleles) ne 'ARRAY') {
+ if(!ref($alleles) || (ref($alleles) ne 'ARRAY')) {
throw('Reference to a list of Bio::EnsEMBL::Variation::AlleleFeature objects is required');
}
@@ -185,14 +186,16 @@ sub type_variation {
return [];
}
- my @features = $tr->fetch_all_regulatory_features();
+ my @features = @{$tr->fetch_all_regulatory_features()};
#regulatory_features and consequence_type feature are all in genomic coordinates,
- #so just to check whether they overlap with each other or not
- foreach my $feature (@features) {
- if ($var->end >= $feature->start and $var->start <= $feature->end) {
- $var->regulatory_region('REGULATORY_REGION');
- last;
+ #so just to check whether they overlap with each other or not also in same strand
+ if (@features) {
+ foreach my $feature (@features) {
+ if ($var->end >= $feature->start and $var->start <= $feature->end and $var->strand == $feature->strand) {
+ $var->regulatory_region('REGULATORY_REGION');
+ last;
+ }
}
}
--
GitLab