#!/usr/bin/env perl
# 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.


use strict;
use warnings;

use Bio::EnsEMBL::Registry;


#
# This script show how to fetch a Compara DNAFrag object, that can linked
# to a core Slice object (for example to find genes)
#

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

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



# get compara DBAdaptor
my $comparaDBA = Bio::EnsEMBL::Registry->get_DBAdaptor('Multi', 'compara');

# get GenomeDB for human
my $humanGDB = $comparaDBA->get_GenomeDBAdaptor->fetch_by_registry_name("human");

# get dnafrag for human chr 18
my $dnafrag = $comparaDBA->get_DnaFragAdaptor->fetch_by_GenomeDB_and_name($humanGDB, '18');

# get its core Slice and subslice it
my $slice = $dnafrag->slice;
$slice = $slice->sub_Slice(75000000,76000000,1);

# the the genes on the subslice and print
my $genes = $slice->get_all_Genes;
foreach my $gene (@{$genes}) {
  printf("%s\n", $gene->stable_id);
}