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Summary

Bio::EnsEMBL::Funcgen::Utils::Encode - provides some handy methods to deal
with Encode regions.

Package variables

Included modules

Inherit

Exporter

Synopsis

    use Bio::EnsEMBL::Funcgen::Utils::Encode qw(get_encode_regions);

    my $encode_regions = &get_encode_regions($dnadb, $assembly_version);

Description

Methods

Methods description

  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);

Methods code

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;

}

General documentation

Stefan Graf <graef@ebi.ac.uk>, EMBL-EBI, Ensembl Functional Genomics
This module is part of the Ensembl project:

Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk