From 0f97a58b8869b87616b6975ae944e3fe7af50fbe Mon Sep 17 00:00:00 2001
From: Yuan Chen <yuan@sanger.ac.uk>
Date: Mon, 3 Nov 2008 13:34:32 +0000
Subject: [PATCH] remove calculation for regulatory_region here and calculate
all in parallel_transcript_variation.pl
---
.../Bio/EnsEMBL/Utils/TranscriptAlleles.pm | 24 -------------------
1 file changed, 24 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
index 054f784910..4e5e2046ce 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
@@ -254,30 +254,6 @@ sub type_variation {
throw("Not possible to calculate the consequence type for ",ref($var)," : Bio::EnsEMBL::Variation::ConsequenceType object expected");
}
- ##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
- 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;
- foreach my $f (@{$efa->fetch_all_by_Slice($tr->feature_Slice)}) {
- if ($f->feature_set->name =~ /VISTA\s+enhancer\s+set/i or $f->feature_set->name =~ /cisRED\s+group\s+motifs/i) {
- push @rf, $f;
- }
- }
-
- push @rf, @{$rfa->fetch_all_by_Slice($tr->feature_Slice)};
- foreach my $rf (@rf){
- my $rf_start = $rf->start;
- my $rf_end = $rf->end;
-
- if ($var->end >= $rf_start and $var->start <= $rf_end) {
- $var->type('REGULATORY_REGION') if (!defined $var->type || $var->type !~ /REGULATORY/);
- # print $var->start, " has regulatiory_region near",$tr->dbID,"\n";
- last;
- }
- }
- }
if (($var->start < $tr->start - $UPSTREAM) || ($var->end > $tr->end + $DOWNSTREAM)){
#since the variation is more than UPSTREAM and DOWNSTREAM of the transcript, there is no effect in the transcript
--
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