=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@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
$Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature::VERSION = '112.0.0_57'; # TRIAL
$Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature::VERSION = '112.0.057';
use strict;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _convert_single {
my ($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;