Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_exon
<![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_exon
=head1 SYNOPISIS
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_exon;
use strict;
use vars qw(@ISA %GTF_ENS_PHASE);
use Bio::EnsEMBL::Utils::Converter;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::DnaPepAlignFeature;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
BEGIN {
%GTF_ENS_PHASE = (
0 => 0,
1 => 2,
2 => 1,
'.' => -1
);
}
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
$self->{_bio_ens_seqFeature} = new Bio::EnsEMBL::Utils::Converter (
-in => 'Bio::SeqFeature::Generic',
-out => 'Bio::EnsEMBL::SeqFeature',
);
$self->{_bio_ens_featurePair} = new Bio::EnsEMBL::Utils::Converter (
-in => 'Bio::SeqFeature::FeaturePair',
-out => 'Bio::EnsEMBL::FeaturePair'
);
}
sub _attach_supporting_feature {
my ($self, $exon, $ens_exon) = @_;
unless($exon->has_tag('supporting_feature')){
return;
}
my ($sf) = $exon->each_tag_value('supporting_feature');
unless(defined $sf){
$self->warn("no supporting feature is attached in exon");
return;
}
# $self->{_bio_ens_seqFeature}->contig($self->contig);
$self->{_bio_ens_seqFeature}->analysis($self->analysis);
my $ens_f1 = $self->{_bio_ens_seqFeature}->_convert_single($sf->feature1);
my $ens_f2 = $self->{_bio_ens_seqFeature}->_convert_single($sf->feature2);
$self->{_bio_ens_featurePair}->contig($self->contig);
$self->{_bio_ens_featurePair}->analysis($self->analysis);
my $ens_sf = $self->{_bio_ens_featurePair}->_convert_single($sf);
my @align_feautre_args = (
-feature1 => $ens_f1,
-feature2 => $ens_f2,
-features => [$ens_sf]
);
my $ens_supporting_feature =
Bio::EnsEMBL::DnaPepAlignFeature->new(@align_feautre_args);
$ens_exon->add_supporting_features($ens_supporting_feature);
}
sub _convert_single {
my ($self, $arg) = @_;
unless($arg && $arg->isa('Bio::SeqFeature::Gene::Exon')){
$self->throw("a Bio::SeqFeature::Gene::Exon object needed");
}
my $exon = $arg;
my $ens_exon = Bio::EnsEMBL::Exon->new_fast(
$self->contig, $exon->start, $exon->end, $exon->strand);
my ($phase) = $exon->each_tag_value('phase');
$ens_exon->phase($GTF_ENS_PHASE{$phase});
my $ens_end_phase = 3 - ($exon->length - $phase) % 3;
$ens_end_phase = 0 if $ens_end_phase == 3;
$ens_exon->end_phase($ens_end_phase);
if($self->contig->isa('Bio::EnsEMBL::RawContig')){
$ens_exon->sticky_rank(1);
}
$self->_attach_supporting_feature($exon, $ens_exon);
return $ens_exon;
}
1;
]]>