=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
=cut
$Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::VERSION = '112.0_53'; # TRIAL
$Bio::EnsEMBL::Utils::Converter::bio_ens_hsp::VERSION = '112.053';
use strict;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
# After super initialized, analysis and contig are ready.
my $bio_ens_seqFeature_converter = new Bio::EnsEMBL::Utils::Converter(
-in => 'Bio::SeqFeature::Generic',
-out => 'Bio::EnsEMBL::SeqFeature',
-analysis => $self->analysis,
-contig => $self->contig
);
$self->_bio_ens_seqFeature_converter($bio_ens_seqFeature_converter);
}
sub _convert_single {
my ($self, $hsp) = @_;
unless(ref($hsp) && $hsp->isa('Bio::Search::HSP::GenericHSP')){
$self->throw("a GenericHSP object needed");
}
my $in = $self->in;
my $out = $self->out;
if($out =~ /^Bio::EnsEMBL::ProteinFeature$/){
return $self->_convert_single_to_proteinFeature($hsp);
}elsif($out =~/^Bio::EnsEMBL::(DnaDna|DnaPep|PepDna)AlignFeature/){
return $self->_convert_single_to_alignFeature($hsp);
}else{
$self->throw("[$in]->[$out], not implemented");
}
}
sub _convert_single_to_featurePair {
my ($self, $hsp) = @_;
my $bio_ens_seqFeature_converter = $self->_bio_ens_seqFeature_converter;
my $ens_feature1 = $bio_ens_seqFeature_converter->_convert_single(
$hsp->feature1);
my $ens_feature2 = $bio_ens_seqFeature_converter->_convert_single(
$hsp->feature2);
$ens_feature1->p_value($hsp->evalue);
$ens_feature1->score($hsp->score);
$ens_feature1->percent_id($hsp->percent_identity);
$ens_feature2->p_value($hsp->evalue);
$ens_feature2->score($hsp->score);
$ens_feature2->percent_id($hsp->percent_identity);
my $featurePair = Bio::EnsEMBL::FeaturePair->new(
-feature1 => $ens_feature1,
-feature2 => $ens_feature2
);
return $featurePair;
}
sub _convert_single_to_proteinFeature {
my ($self, $hsp) = @_;
my $ens_featurePair = $self->_convert_single_to_featurePair($hsp);
my $ens_proteinFeature = Bio::EnsEMBL::ProteinFeature->new(
-feature1 => $ens_featurePair->feature1,
-feature2 => $ens_featurePair->feature2
);
$ens_proteinFeature->seqname($self->translation_id);
return $ens_proteinFeature;
}
sub _convert_single_to_alignFeature {
my ($self, $hsp) = @_;
my $ens_featurePair = $self->_convert_single_to_featurePair($hsp);
my $cigar_string = $hsp->cigar_string;
my @args = (
-feature1 => $ens_featurePair->feature1,
-feature2 => $ens_featurePair->feature2,
-cigar_string => $hsp->cigar_string
);
my $contig = $self->contig;
# choose the AlignFeature based on the blast program
my $program = $hsp->algorithm;
$self->throw("HSP does not have algorithm value") unless(defined($program));
my $align_feature;
if($program =~ /blastn/i){
$align_feature = new Bio::EnsEMBL::DnaDnaAlignFeature(@args);
# $align_feature->attach_seq($contig);
}elsif($program =~ /blastx/i){
$align_feature = new Bio::EnsEMBL::DnaPepAlignFeature(@args);
# $align_feature->attach_seq($contig);
}else{
$self->throw("\[$program\] is not supported yet");
}
return $align_feature;
}
sub _bio_ens_seqFeature_converter {
my ($self) = shift ;
return $self->{_bio_ens_seqFeature_converter} = shift if(@_);
return $self->{_bio_ens_seqFeature_converter};
}
1;