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lib/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm  view on Meta::CPAN

use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Converter::bio_ens;
use Bio::EnsEMBL::DnaDnaAlignFeature;
use Bio::EnsEMBL::DnaPepAlignFeature;
use Bio::EnsEMBL::PepDnaAlignFeature;
use Bio::EnsEMBL::ProteinFeature;

@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, $input) = @_;
    
    my $in = $self->in;
    my $out = $self->out;
    
    if($in =~ /Bio::Search::Hit::GenericHit/){
        return $self->_convert_single_hit($input);
    }elsif($in =~ /Bio::Search::HSP::GenericHSP/){
        return $self->_convert_single_hsp($input);
    }else{
        $self->throw("[$in]->[$out], not implemented");
    }
}

sub _convert_single_hit {


}

sub _convert_single_hsp {
    my ($self, $hsp) = @_;

    unless(ref($hsp) && $hsp->isa('Bio::Search::HSP::GenericHSP')){
        $self->throw("a GenericHSP object needed");
    }

    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 $cigar_string = $hsp->cigar_string;
    my @args = (
        -feature1 => $ens_feature1,
        -feature2 => $ens_feature2,
        -cigar_string => $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;
}

# an internal getter/setter for a converter used for seq feature conversion.

sub _bio_ens_seqFeature_converter {
    my ($self, $arg) = @_;
    if(defined $arg){
        $self->{_bio_ens_seqFeature_converter} = $arg;
    }
    return $self->{_bio_ens_seqFeature_converter};
}

1;