Commit 1fa4fa52 authored by Daniel Rios's avatar Daniel Rios
Browse files

added condition to check there is a funcgen database for the variation...

added condition to check there is a funcgen database for the variation database before checking for regulatory features
parent 630c70e3
...@@ -268,9 +268,8 @@ sub type_variation { ...@@ -268,9 +268,8 @@ sub type_variation {
# } # }
# } # }
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 $rfa = $dbFunc->get_ExternalFeatureAdaptor(); my $rfa = $dbFunc->get_ExternalFeatureAdaptor();
foreach my $rf (@{$rfa->fetch_all_by_Slice($tr->feature_Slice)}){ foreach my $rf (@{$rfa->fetch_all_by_Slice($tr->feature_Slice)}){
next if (($rf->feature_set->name !~ /miRNA/) && ($rf->feature_set->name !~ /cisRED/)); next if (($rf->feature_set->name !~ /miRNA/) && ($rf->feature_set->name !~ /cisRED/));
......
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