=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
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
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=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
$Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair::VERSION = '112.0.0_58'; # TRIAL
$Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair::VERSION = '112.0.058';
use strict;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Utils::Converter::ens_bio);
sub _convert_single {
my ($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;