ens_bio_featurePair.pm

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=head1 LICENSE
 
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Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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     http://www.apache.org/licenses/LICENSE-2.0
 
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=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
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=head1 AUTHOR
 
Juguang Xiao <juguang@fugu-sg.org>
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair
 
=head1 SYNOPISIS
 
=head1 DESCRIPTION
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair;
 
use strict;
use vars qw(@ISA);
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::FeaturePair;
use Bio::EnsEMBL::Utils::Converter::ens_bio;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::ens_bio);
 
sub _convert_single {
    my ($self, @args) = @_;
 
}
 
# convert object from Bio::EnsEMBL::RepeatFeature
# to Bio::SeqFeature::FeaturePair
 
sub _convert_single_repeatFeature {
    my ($self, $ens_repeat) = @_;
    
    my $feature1 = new Bio::SeqFeature::Generic(
        -start => $ens_repeat->start,
        -end => $ens_repeat->end,
        -strand => $ens_repeat->strand,
        -source_tag => $ens_repeat->source_tag
        -primary_tag => $ens_repeat->repeat_class,
        -seq_id => $ens_repeat->seqname
    );
    
    my ($start2, $end2);
    if($ens_repeat->strand == 1){
        $start2 = $ens_repeat->hstart;
        $end2 = $ens_repeat->hend;
    }elsif($ens_repeat->strand == -1){
        $start2 = $ens_repeat->hend;
        $end2 = $ens_repeat->hstart;
    }else{
        $self->throw("strand cannot be out of range (1, -1)");
    }
        
    my $feature2 = new Bio::SeqFeature::Generic(
        -start => $start2,
        -end => $end2,
        -source_tag => $ens_repeat->source_tag,
        -primary_tag => $ens_repeat->repeat_class,
        -seq_id => $ens_repeat->repeat_name
    );
    
    my $output_module = $self->out;
    eval "require $output_module"; ## no critic
    return new Bio::SeqFeature::FeaturePair(
        -feature1 => $feature1,
        -feature2 => $feature2
    );
}
 
1;