Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_transcript
<![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_transcript - the instance converter
=head1 SYNOPISIS
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_transcript;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _convert_single {
my ($self, $arg) = @_;
unless($arg->isa('Bio::SeqFeature::Gene::Transcript')){
$self->throw("A Bio::SeqFeature::Gene::Transcript object needed");
}
my $transcript = $arg;
my @exons = $transcript->exons_ordered;
$self->{_converter_for_exons}->contig($self->contig);
$self->{_converter_for_exons}->analysis($self->analysis);
my $ens_exons = $self->{_converter_for_exons}->convert(\@exons);
my $ens_transcript = Bio::EnsEMBL::Transcript->new(@{$ens_exons});
$ens_transcript->start($transcript->start);
$ens_transcript->end($transcript->end);
# $ens_transcript->strand($transcript->strand);
return $ens_transcript;
}
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
$self->{_converter_for_exons} = new Bio::EnsEMBL::Utils::Converter(
-in => 'Bio::SeqFeature::Gene::Exon',
-out => 'Bio::EnsEMBL::Exon'
);
}
]]>