Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_gene
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=head1 AUTHOR
Juguang Xiao <juguang@tll.org.sg>
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Converter::bio_ens_gene
=head1 SYNOPISIS
=head1 DESCRIPTION
This module is to convert from objects of
Bio::SeqFeature::Gene::GeneStructure to those of Bio::EnsEMBL::Gene
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_gene;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
$self->{_converter_for_transcripts} = new Bio::EnsEMBL::Utils::Converter(
-in => 'Bio::SeqFeature::Gene::Transcript',
-out => 'Bio::EnsEMBL::Transcript'
);
}
sub _convert_single {
my ($self, $input) = @_;
unless($input->isa('Bio::SeqFeature::Gene::GeneStructure')){
$self->throw("a Bio::SeqFeature::Gene::GeneStructure object needed");
}
my $gene = $input;
my $ens_gene = Bio::EnsEMBL::Gene->new();
$ens_gene->analysis($self->analysis);
my @transcripts = $gene->transcripts;
# contig is needed by exon and Supporting Feature; S.F. needs an analysis.
$self->{_converter_for_transcripts}->contig($self->contig);
$self->{_converter_for_transcripts}->analysis($self->analysis);
my $ens_transcripts = $self->{_converter_for_transcripts}->convert(
\@transcripts);
foreach(@{$ens_transcripts}){
$ens_gene->add_Transcript($_);
}
return $ens_gene;
}
1;
]]>