Bio::EnsEMBL::Utils::Converter bio_ens_transcript
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Summary
Bio::EnsEMBL::Utils::Converter::bio_ens_transcript - the instance converter
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Transcript
Bio::EnsEMBL::Utils::Converter::bio_ens
Inherit
Bio::EnsEMBL::Utils::Converter::bio_ens
Synopsis
No synopsis!
Description
Methods
_convert_single
No description
Code
_initialize
No description
Code
Methods description
None available.
Methods code
_convert_singledescriptionprevnextTop
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 $ens_transcript;
}
_initializedescriptionprevnextTop
sub _initialize {
    my ($self, @args) = @_;
    $self->SUPER::_initialize(@args);

    $self->{_converter_for_exons} = new Bio::EnsEMBL::Utils::Converter(
        -in => 'Bio::SeqFeature::Gene::Exon',
        -out => 'Bio::EnsEMBL::Exon'
    );
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.
AUTHORTop
Juguang Xiao <juguang@tll.org.sg>
SYNOPISISTop