Code which looks for sequence regions in the Aedes database from Ensembl Metazoa

extracting_seqregions.pl

use strict;
use warnings;

use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(
	-host=>'mysql.ebi.ac.uk',
	-user=>'anonymous',
	-port=>4157,
	-db_version => 61
);

my $name = 'Aedes aegypti';
my $assembly = 'AaegL1';
my $cs_name = 'supercontig';
my $chromosome_name= 'supercont1.1';
my $start_pos = 5248294;
my $end_pos = 5248380;

my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($name, 'core');
my $sa = $dba->get_SliceAdaptor();

#Showing what is available for this species
my $toplevel_slices = $sa->fetch_all('toplevel');
my $seqlevel_slices = $sa->fetch_all('seqlevel');

my %top_cs = map { $_->coord_system_name, 1 } @{$toplevel_slices};
my %seq_cs = map { $_->coord_system_name, 1 } @{$seqlevel_slices};

print 'Available toplevel coordinate systems: ', join(',', keys %top_cs), "\n";
print 'Available seqlevel coordinate systems: ', join(',', keys %seq_cs), "\n";

foreach my $s (@{$toplevel_slices}) {
  print $s->name(), "\n";
}

#Taking the values given originally to find a slice
print '=' x 20, "\n";
my $region = $sa->fetch_by_region('toplevel', $chromosome_name, $start_pos, $end_pos);
print $region->name, "\n";
#or can use the coord system name
$region = $sa->fetch_by_region($cs_name, $chromosome_name, $start_pos, $end_pos);
print $region->name, "\n";