bio_ens_exon.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
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distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=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;
}
 
 
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