From 47ed19f29e8f6419b7f140e5ef14c8d0d3a0e017 Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Mon, 28 Jul 2008 10:32:06 +0000
Subject: [PATCH] added condition to check for regulatory features only if
there is a FuncGen database
---
modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
index 88637dee35..f6f6cb3154 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
@@ -255,9 +255,8 @@ sub type_variation {
}
##to find if a SNP is overlapping with the transcript of the regulatory region, also the SNP should be within 5kb on both side of the transcript, then check whether they overlapping
-
- if ($tr and ref($tr) and $tr->isa('Bio::EnsEMBL::Transcript')) {
- my $dbFunc = $tr->adaptor->db->get_db_adaptor("funcgen");
+ my $dbFunc = $tr->adaptor->db->get_db_adaptor("funcgen");
+ if ($tr and ref($tr) and $tr->isa('Bio::EnsEMBL::Transcript') and (defined $dbFunc)) {
my $efa = $dbFunc->get_ExternalFeatureAdaptor();
my $rfa = $dbFunc->get_RegulatoryFeatureAdaptor();
my @rf;
--
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