Commit 52b6acec authored by Daniel Rios's avatar Daniel Rios
Browse files

modified to use funcgen database to calculate snps in regulatory regions

parent bbb81025
...@@ -268,14 +268,19 @@ sub type_variation { ...@@ -268,14 +268,19 @@ sub type_variation {
# } # }
# } # }
if ($tr and ref($tr) and $tr->isa('Bio::EnsEMBL::Transcripts')) {
foreach my $rf (@{$tr->fetch_all_regulatory_features()}) { if ($tr and ref($tr) and $tr->isa('Bio::EnsEMBL::Transcript')) {
my $dbFunc = $tr->adaptor->db->get_db_adaptor("funcgen");
my $rfa = $dbFunc->get_ExternalFeatureAdaptor();
foreach my $rf (@{$rfa->fetch_all_by_Slice($tr->feature_Slice)}){
next if (($rf->feature_set->name !~ /miRNA/) && ($rf->feature_set->name !~ /cisRED/));
# foreach my $rf (@{$tr->fetch_all_regulatory_features()}) {
my $rf_start = $rf->start; my $rf_start = $rf->start;
my $rf_end = $rf->end; my $rf_end = $rf->end;
if ($var->end >= $rf_start and $var->start <= $rf_end) { if ($var->end >= $rf_start and $var->start <= $rf_end) {
$var->type('REGULATORY_REGION') if ($var->type !~ /REGULATORY/); $var->type('REGULATORY_REGION') if (!defined $var->type || $var->type !~ /REGULATORY/);
print $var->start, " has regulatiory_region near",$tr->dbId,"\n"; # print $var->start, " has regulatiory_region near",$tr->dbID,"\n";
last; last;
} }
} }
......
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