#!/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',
);

# Regulatory Features 
# Using the human DB, fetch the all the cell type specific regulatory features with stable ID 'ENSR00000623613'.
# Print out the stable ID, bound_start/end and start/end values, name of the cell and feature type for each.
# HINT: To get all the cell type specific RegulatoryFeatures use the fetch_all_by_stable_ID method.

#Grab the regfeat adaptor
my $regfeat_adaptor = $registry->get_adaptor('Human', 'funcgen', 'regulatoryfeature');


#Fetch ENSR00000623613 reg feats for all cell types.
my @rfs = @{$regfeat_adaptor->fetch_all_by_stable_ID('ENSR00000623613')};


# Print out the details
foreach my $rf(@rfs){
  print $rf->stable_id.": \n";
  print "\tRelative Position: ".$rf->bound_start."..".$rf->start."-".$rf->end."..".$rf->bound_end."\n";
  print "\tCell: ".$rf->cell_type->name."\n";
  print "\tFeature Type: ".$rf->feature_type->name."\n";
}

__END__


ENSR00000623613: 
        Relative Position: 27178100..27178438-27185061..27186300
        Cell: K562
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27123400..27178438-27185061..27297450
        Cell: H1ESC
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27177575..27178438-27185061..27187569
        Cell: HUVEC
        Feature Type: Gene Associated
ENSR00000623613: 
        Relative Position: 27177907..27178438-27185061..27185882
        Cell: HMEC
        Feature Type: Promoter Associated
ENSR00000623613: 
        Relative Position: 27126300..27178438-27185061..27270800
        Cell: NH-A
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27178438..27178438-27185061..27185061
        Cell: HeLa-S3
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27178438..27178438-27185061..27187350
        Cell: HepG2
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27178050..27178438-27185061..27187700
        Cell: IMR90
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27178438..27178438-27185061..27185061
        Cell: HSMM
        Feature Type: Promoter Associated
ENSR00000623613: 
        Relative Position: 27178438..27178438-27185061..27185061
        Cell: MultiCell
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27177500..27178438-27185061..27187050
        Cell: NHEK
        Feature Type: Unclassified
ENSR00000623613: 
        Relative Position: 27177650..27178438-27185061..27185061
        Cell: GM12878
        Feature Type: Unclassified