diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/Utils/Encode.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Utils/Encode.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,96 @@
+# Ensembl module for Bio::EnsEMBL::Funcgen::Utils::Encode
+#
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2011 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+
+=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, $assembly_version);
+
+=head1 DESCRIPTION
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::Utils::Encode;
+
+require Exporter;
+use vars qw(@ISA @EXPORT_OK);
+@ISA = qw(Exporter);
+@EXPORT_OK = qw(get_encode_regions);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+use POSIX;
+use Data::Dumper;
+
+=head2 get_encode_regions
+
+  Arg [1]     : Bio::EnsEMBL::DBSQL::DBAdaptor
+  Description : fetch encode region coordinates from core db
+  Returns     : reference to list of Bio::EnsEMBL::MiscFeatures Encode region slices
+  Exceptions  : Throws if no Bio::EnsEMBL::DBSQL::DBAdaptor defined
+  Example     : get_encode_regions($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;