Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene
<![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_predictionGene
=head1 SYNOPISIS
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Converter;
use Bio::EnsEMBL::PredictionTranscript;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _initialize {
my ($self, @args) = @_;
$self->{_predictionExonConverter} = new Bio::EnsEMBL::Utils::Converter(
-in => 'Bio::SeqFeature::Gene::Exon',
-out => 'Bio::EnsEMBL::Exon',
);
$self->SUPER::_initialize(@args);
$self->{_predictionExonConverter}->contig($self->contig);
$self->{_predictionExonConverter}->analysis($self->analysis);
}
sub _convert_single {
my ($self, $input) = @_;
$self->throw("one argument needed") unless($input and defined($input));
$self->throw("a Bio::Tools::Prediction::Gene object needed")
unless(ref($input) && $input->isa('Bio::Tools::Prediction::Gene'));
my $output = Bio::EnsEMBL::PredictionTranscript->new;
$output->analysis($self->analysis);
my @exons = sort {$a->start <=> $b->start} $input->exons;
# Not sure on the correctivity of phase calculation.
my $previous_end_phase = -1;
foreach(@exons){
my $length = $_->length;
my $frame = $_->frame;
my $phase = ($previous_end_phase+1) %3;
my $end_phase = ($length-$frame) %1;
$previous_end_phase = $end_phase;
$_->add_tag_value("phase", $phase);
$_->add_tag_value("end_phase", $end_phase);
}
my @ens_exons = @{$self->{_predictionExonConverter}->convert(\@exons)};
$output->add_Exon($_) foreach(@ens_exons);
return $output;
}
=head2 contig
Title : contig
Usage : $self->contig
Function: get and set for contig
Return : L<Bio::EnsEMBL::RawContig>
Args : L<Bio::EnsEMBL::RawContig>
=cut
sub contig {
my ($self, $arg) = @_;
if(defined($arg)){
$self->throws("A Bio::EnsEMBL::RawContig object expected.") unless(defined $arg);
$self->{_contig} = $arg;
# assign it to the sub converter which converts exons
$self->{_predictionExonConverter}->contig($arg);
}
return $self->{_contig};
}
1;
]]>