Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_transcript =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' ); }