From 3f29d10989bd9a377b932bf3629865ea8a508b85 Mon Sep 17 00:00:00 2001
From: Yuan Chen <yuan@sanger.ac.uk>
Date: Mon, 17 Oct 2005 15:33:15 +0000
Subject: [PATCH] update
---
.../Bio/EnsEMBL/Utils/TranscriptAlleles.pm | 45 +++++++++++++------
1 file changed, 31 insertions(+), 14 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
index 91ab625ff2..f4fe609a48 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
@@ -89,7 +89,7 @@ sub get_all_ConsequenceType {
# my $new_allele = $allele->transform('chromosome');
my $consequence_type = Bio::EnsEMBL::Variation::ConsequenceType->new($transcript->dbID(),'',$allele->start,$allele->end,$allele->strand,[$allele->allele_string]);
#calculate the consequence type of the Allele
- my $ref_consequences = type_variation($transcript,$consequence_type);
+ my $ref_consequences = type_variation($transcript,"",$consequence_type);
if ($allele->start != $allele->end){
#do not calculate for indels effects of 2 or more in same codon
push @out, @{$ref_consequences};
@@ -172,6 +172,7 @@ sub calculate_same_codon{
#
sub type_variation {
my $tr = shift;
+ my $g = shift;
my $var = shift;
my $UPSTREAM = 5000;
@@ -181,24 +182,40 @@ sub type_variation {
throw("Not possible to calculate the consequence type for ",ref($var)," : Bio::EnsEMBL::Variation::ConsequenceType object expected");
}
- if (($var->start < $tr->start - $UPSTREAM) || ($var->end > $tr->end + $DOWNSTREAM)){
- #since the variation is more than UPSTREAM and DOWNSTREAM of the transcript, there is no effect in the transcript
- return [];
- }
+ ##to find if a SNP is overlapping with a regulatory region, we need to get a slice containing a gene
+ ##plus 5kb on both side, then fetch regulatory feature by the slice, then check whether they overlapping
+
+ if ($g and ref($g) and $g->isa('Bio::EnsEMBL::Gene')) {
+
+ my $seq_region_slice = $g->slice->seq_region_Slice;
+
+ my $g_start = $g->start - $UPSTREAM;
+ $g_start = 1 if $g_start <1;
+ my $g_end = $g->end + $DOWNSTREAM;
+ $g_end = $seq_region_slice->end if $g_end > $seq_region_slice->end;
+
+ my $g_slice = $seq_region_slice->sub_Slice($g_start,$g_end, $g->slice->strand);
- my @features = @{$tr->fetch_all_regulatory_features()};
+ my $rfa = $g->adaptor->db->get_RegulatoryFeatureAdaptor();
- #regulatory_features and consequence_type feature are all in genomic coordinates,
- #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');
+ my $rfs = $rfa->fetch_all_by_Slice($g_slice);
+
+ foreach my $rf (@{$rfs}) {
+ my $new_rf_start = $rf->start+$g_slice->start-1;
+ my $new_rf_end = $rf->end+$g_slice->start-1;
+
+ if ($var->end >= $new_rf_start and $var->start <= $new_rf_end) {
+ $var->regulatory_region('REGULATORY_REGION');
last;
}
}
}
+ if (($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
+ return [];
+ }
+
my $tm = $tr->get_TranscriptMapper();
my @coords = $tm->genomic2cdna($var->start,
$var->end,
@@ -216,7 +233,7 @@ sub type_variation {
my %new_var = %{$var};
$new_var{'end'} = $var->start + $c->length() - 1;
$var->start( $new_var{'end'} + 1);
- push @out, @{type_variation($tr, bless \%new_var, ref($var))};
+ push @out, @{type_variation($tr, "", bless \%new_var, ref($var))};
}
return \@out;
@@ -283,7 +300,7 @@ sub type_variation {
my %new_var = %{$var};
$new_var{'end'} = $var->start + $c->length() - 1;
$var->start( $new_var{'end'} + 1);
- push @out, @{type_variation($tr, bless \%new_var, ref($var))};
+ push @out, @{type_variation($tr, "", bless \%new_var, ref($var))};
}
return \@out;
}
--
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