Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair
<![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_featurePair
=head1 SYNOPISIS
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::RepeatConsensus;
use Bio::EnsEMBL::ProteinFeature;
use Bio::EnsEMBL::Utils::Converter;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
my ($translation_id) = $self->_rearrange([qw(TRANSLATION_ID)], @args);
$self->translation_id($translation_id);
# internal converter for seqFeature
$self->{_bio_ens_seqFeature} = new Bio::EnsEMBL::Utils::Converter (
-in => 'Bio::SeqFeature::Generic',
-out => 'Bio::EnsEMBL::SeqFeature',
);
}
sub _convert_single {
my ($self, $pair) = @_;
unless($pair && $pair->isa('Bio::SeqFeature::FeaturePair')){
$self->throw('a Bio::SeqFeature::FeaturePair object needed');
}
if($self->out eq 'Bio::EnsEMBL::RepeatFeature'){
return $self->_convert_single_to_repeatFeature($pair);
}elsif($self->out eq 'Bio::EnsEMBL::FeaturePair'){
return $self->_convert_single_to_featurePair($pair);
}elsif($self->out eq 'Bio::EnsEMBL::ProteinFeature'){
return $self->_convert_single_to_proteinFeature($pair);
}else{
my $output_module = $self->out;
$self->throw("Cannot covert to [$output_module]");
}
}
sub _convert_single_to_featurePair {
my ($self, $pair) = @_;
my $feature1 = $pair->feature1;
my $feature2 = $pair->feature2;
$self->{_bio_ens_seqFeature}->contig($self->contig);
$self->{_bio_ens_seqFeature}->analysis($self->analysis);
my $ens_f1 = $self->{_bio_ens_seqFeature}->_convert_single($feature1);
my $ens_f2 = $self->{_bio_ens_seqFeature}->_convert_single($feature2);
my $ens_fp = Bio::EnsEMBL::FeaturePair->new(
-feature1 => $ens_f1,
-feature2 => $ens_f2
);
return $ens_fp;
}
sub _convert_single_to_proteinFeature {
my ($self, $pair) = @_;
my $featurePair = $self->_convert_single_to_featurePair($pair);
my $proteinFeature = Bio::EnsEMBL::ProteinFeature->new(
-feature1 => $featurePair->feature1,
-feature2 => $featurePair->feature2
);
$proteinFeature->seqname($self->translation_id);
return $proteinFeature;
}
sub _convert_single_to_repeatFeature {
my ($self, $pair) = @_;
my $feature1 = $pair->feature1;
my $feature2 = $pair->feature2;
my $ens_repeatfeature = new Bio::EnsEMBL::RepeatFeature(
-seqname => $feature1->seq_id,
-start => $feature1->start,
-end => $feature1->end,
-strand => $feature1->strand,
-source_tag => $feature1->source_tag,
);
my ($h_start, $h_end);
if($feature1->strand == 1){
$h_start = $feature2->start;
$h_end = $feature2->end;
}elsif($feature1->strand == -1){
$h_start = $feature2->end;
$h_end = $feature2->start;
}else{
$self->throw("strand cannot be outside of (1, -1)");
}
$ens_repeatfeature->hstart($h_start);
$ens_repeatfeature->hend($h_end);
my $repeat_name = $feature2->seq_id;
my $repeat_class = $feature1->primary_tag;
$repeat_class ||= $feature2->primary_tag;
$repeat_class ||= "not sure";
my $ens_repeat_consensus =
$self->_create_consensus($repeat_name, $repeat_class);
$ens_repeatfeature->repeat_consensus($ens_repeat_consensus);
my($contig) = ref ($self->contig) eq 'ARRAY' ? @{$self->contig} : $self->contig;
$ens_repeatfeature->attach_seq($contig);
$ens_repeatfeature->analysis($self->analysis);
return $ens_repeatfeature;
}
sub _create_consensus{
my ($self, $repeat_name, $repeat_class) = @_;
my $consensus = new Bio::EnsEMBL::RepeatConsensus;
$consensus->name($repeat_name);
$consensus->repeat_class($repeat_class);
return $consensus;
}
1;
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