Raw content of Bio::EnsEMBL::Utils::Converter::ens_bio_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>.
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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 = $self->out;
require "$output_module";
return new Bio::SeqFeature::FeaturePair(
-feature1 => $feature1,
-feature2 => $feature2
);
}
1;
]]>