Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature
<![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
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=head1 AUTHOR
Juguang Xiao <juguang@tll.org.sg>
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature
=head1 SYNOPISIS
Please read Bio::EnsEMBL::Utils::Converter
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::SeqFeature;
use Bio::EnsEMBL::SimpleFeature;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Converter::bio_ens;
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _convert_single {
my ($self, $in) = @_;
unless($in && defined($in) && $in->isa('Bio::SeqFeature::Generic')){
$self->throw("a Bio::SeqFeature::Generic object needed");
}
my $seqFeature = $in;
my $seq_id = $seqFeature->seq_id;
unless(defined($seq_id) && $seq_id){
$self->warn("No seq_id value. EnsEMBL SeqFeature will validate it");
$seq_id = 'Unknown';
}
# Debated issue here. There are p_value and percent_id in EnsEMBL API and DB
# schema, but not in bioperl. If in bioperl there are tags called p_value or
# percent_id, then the values are passed, otherwise set the default 1.
#
# the problem arise when I try to converter the seqfeature for tmhmm to
# EnsEMBL seqFeature.
# -- Juguang, 11 July '03
my $score = $in->score || 0;
my $percent_id;
if($in->has_tag('percent_id')){
($percent_id) = $in->get_tag_values('percent_id');
}else{
$percent_id ||= 0;
}
my $p_value;
if($in->has_tag('p_value')){
($p_value) = $in->get_tag_values('p_value');
}elsif($in->has_tag('evalue')){
($p_value) = $in->get_tag_values('evalue');
}else{
$p_value ||= 1;
}
my $ens_seqFeature;
my %args = (
-start => $in->start,
-end => $in->end,
-strand => $in->strand,
-score => $score,
-analysis => $self->analysis,
-source_tag => $in->source_tag,
-seqname => $seq_id,
-percent_id => $percent_id,
-p_value => $p_value
);
my $output_module = $self->out;
if($output_module eq 'Bio::EnsEMBL::SeqFeature'){
$ens_seqFeature = new Bio::EnsEMBL::SeqFeature(%args);
}elsif($self->out eq 'Bio::EnsEMBL::SimpleFeature'){
$ens_seqFeature = new Bio::EnsEMBL::SimpleFeature(%args);
# The field that there is in SimpleFeature, but not in SeqFeature.
$ens_seqFeature->display_label('__NONE__');
}elsif($self->out eq 'Bio::EnsEMBL::Exon'){
$ens_seqFeature = Bio::EnsEMBL::Exon->new_fast(
$self->contig, $seqFeature->start, $seqFeature->end,
$seqFeature->strand);
}elsif($self->out eq 'Bio::EnsEMBL::ProteinFeature'){
my $seq_id2 = $self->analysis->logic_name;
unless(defined $self->translation_id){
$self->throw('translation_id unset, in ProteinFeature conversion');
}
$args{'-seqname'} = $self->translation_id;
$ens_seqFeature = Bio::EnsEMBL::ProteinFeature->new(
-feature1 => Bio::EnsEMBL::SeqFeature->new(%args),
-feature2 => Bio::EnsEMBL::SeqFeature->new(
-start => 0,
-end => 0,
-seqname => $seq_id2
)
);
}else{
$self->throw("[$output_module] as -out, not supported");
}
$ens_seqFeature->attach_seq($self->contig);
return $ens_seqFeature;
}
1;
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