#!/usr/bin/env perl

=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

=cut

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
);

#1. External Features
#The funcgen DB contains some data directly imported from external sources, like predicted miRNA targets from miRanda, predicted regulatory regions from cisRED, or experimentally verified regulatory regions from EnhancerDB
#Create a script which gets all the 'cisRED motifs' features for the Human region 7:27136000-27139000.
#List their display_labels. List all active regions from EnhancerDB ('VISTA enhancer set') for Human chromosome 7.
#Hint - use their feature type to know which ones are active


#Grab the eFG adaptor
my $sa = $registry->get_adaptor('Human', 'core', 'slice');
my $fsa = $registry->get_adaptor('Human', 'funcgen', 'featureset');

my $cisred_slice = $sa->fetch_by_region('chromosome','7',27136000,27139000);
my $cisred_fset = $fsa->fetch_by_name('cisRED motifs');
my @cisred_afs = @{$cisred_fset->get_Features_by_Slice($cisred_slice)};
print "Found ".scalar(@cisred_afs)." cisRED features\n";

foreach my $af (@cisred_afs){
	print $af->display_label."\n";
}


my $vista_fset = $fsa->fetch_by_name('VISTA enhancer set');
my $vista_slice = $sa->fetch_by_region('chromosome','7');
my @vista_afs = @{$vista_fset->get_Features_by_Slice($vista_slice)};

print "Found ".scalar(@vista_afs)." Vista features\n";

foreach my $af (@vista_afs){
	if($af->feature_type->name =~ /Enhancer/){ print $af->display_label."\n"; }
}

__END__

>perl features_1.pl

Found 5 cisRED features
craHsap152694
craHsap152679
craHsap152667
craHsap152648
craHsap152626

Found 5 Vista features
hs169
hs170
hs79
hs174
hs183