Raw content of Bio::EnsEMBL::Funcgen::Utils::Encode
<![CDATA[# Personal Ensembl module for Bio::EnsEMBL::Funcgen::Utils::Encode
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Funcgen::Utils::Encode - provides some handy methods to deal
with Encode regions.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::Utils::Encode qw(get_encode_regions);
my $encode_regions = &get_encode_regions($dnadb, $assembly_version);
=head1 DESCRIPTION
=head1 AUTHOR
Stefan Graf <graef@ebi.ac.uk>, EMBL-EBI, Ensembl Functional Genomics
This module is part of the Ensembl project:
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::Utils::Encode;
require Exporter;
use vars qw(@ISA @EXPORT_OK);
@ISA = qw(Exporter);
@EXPORT_OK = qw(get_encode_regions);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use POSIX;
use Data::Dumper;
=head2 get_encode_regions
Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
Description : fetch encode region coordinates from core db
Returns : reference to list of Bio::EnsEMBL::MiscFeatures Encode region slices
Exceptions : Throws if no Bio::EnsEMBL::DBSQL::DBAdaptor defined
Example : get_encode_regions($dnadb);
=cut
sub get_encode_regions {
my $db = shift;
throw("Need to pass a valid Bio::EnsEMBL::DBSQL::DBAdaptor")
if (! ($db && $db->isa("Bio::EnsEMBL::DBSQL::DBAdaptor")));
my $sa = $db->get_SliceAdaptor();
my $tls = $sa->fetch_all('toplevel');
#map { print Dumper $_->name } @$tls;
my $mfa = $db->get_MiscFeatureAdaptor();
my @encode_regions;
map {
push @encode_regions, @{$mfa->fetch_all_by_Slice_and_set_code($_, 'encode')};
} @$tls;
return \@encode_regions;
#my %encode_regions;
#map { $encode_regions{$_->display_id} = sprintf
# ("%s:%s:%s:%d:%d:%d",
# $_->slice->coord_system_name,
# $_->slice->coord_system()->version(),
# $_->slice->seq_region_name,
# $_->start, $_->end, $_->strand);
# } @encode_regions;
#
#return \%encode_regions;
}
1;
]]>