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1 # Ensembl module for Bio::EnsEMBL::Funcgen::Utils::Encode
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2 #
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3
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4 =head1 LICENSE
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5
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6 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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7 Genome Research Limited. All rights reserved.
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8
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9 This software is distributed under a modified Apache license.
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10 For license details, please see
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11
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12 http://www.ensembl.org/info/about/code_licence.html
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13
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14 =head1 CONTACT
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15
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16 Please email comments or questions to the public Ensembl
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17 developers list at <ensembl-dev@ebi.ac.uk>.
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18
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19 Questions may also be sent to the Ensembl help desk at
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20 <helpdesk@ensembl.org>.
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21
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22
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23 =head1 NAME
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24
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25 Bio::EnsEMBL::Funcgen::Utils::Encode - provides some handy methods to deal
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26 with Encode regions.
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27
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28 =head1 SYNOPSIS
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29
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30 use Bio::EnsEMBL::Funcgen::Utils::Encode qw(get_encode_regions);
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31
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32 my $encode_regions = &get_encode_regions($dnadb, $assembly_version);
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33
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34 =head1 DESCRIPTION
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35
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36 =cut
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37
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38 use strict;
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39 use warnings;
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40
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41 package Bio::EnsEMBL::Funcgen::Utils::Encode;
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42
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43 require Exporter;
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44 use vars qw(@ISA @EXPORT_OK);
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45 @ISA = qw(Exporter);
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46 @EXPORT_OK = qw(get_encode_regions);
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47
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48 use Bio::EnsEMBL::Utils::Exception qw(throw);
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49 use POSIX;
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50 use Data::Dumper;
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51
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52 =head2 get_encode_regions
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53
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54 Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
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55 Description : fetch encode region coordinates from core db
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56 Returns : reference to list of Bio::EnsEMBL::MiscFeatures Encode region slices
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57 Exceptions : Throws if no Bio::EnsEMBL::DBSQL::DBAdaptor defined
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58 Example : get_encode_regions($dnadb);
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59
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60 =cut
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61
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62 sub get_encode_regions {
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63
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64 my $db = shift;
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65
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66 throw("Need to pass a valid Bio::EnsEMBL::DBSQL::DBAdaptor")
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67 if (! ($db && $db->isa("Bio::EnsEMBL::DBSQL::DBAdaptor")));
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68
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69 my $sa = $db->get_SliceAdaptor();
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70 my $tls = $sa->fetch_all('toplevel');
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71 #map { print Dumper $_->name } @$tls;
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72
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73 my $mfa = $db->get_MiscFeatureAdaptor();
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74
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75 my @encode_regions;
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76 map {
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77 push @encode_regions, @{$mfa->fetch_all_by_Slice_and_set_code($_, 'encode')};
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78 } @$tls;
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79
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80 return \@encode_regions;
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81
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82
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83 #my %encode_regions;
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84 #map { $encode_regions{$_->display_id} = sprintf
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85 # ("%s:%s:%s:%d:%d:%d",
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86 # $_->slice->coord_system_name,
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87 # $_->slice->coord_system()->version(),
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88 # $_->slice->seq_region_name,
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89 # $_->start, $_->end, $_->strand);
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90 # } @encode_regions;
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91 #
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92 #return \%encode_regions;
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93
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94 }
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95
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96 1;
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