Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_hit
<![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>.
=cut
=head1 DESCRIPTION
Sequence alignment hits were previously stored within the core database
as ungapped alignments. This imposed 2 major constraints on alignments:
a) alignments for a single hit record would require multiple rows in
the database, and
b) it was not possible to accurately retrieve the exact original alignment.
Therefore, in the new branch sequence alignments are now stored as
ungapped alignments in the cigar line format (where CIGAR stands for
Concise Idiosyncratic Gapped Alignment Report).
In the cigar line format alignments are sotred as follows:
M: Match
D: Deletino
I: Insertion
An example of an alignment for a hypthetical protein match is shown
below:
Query: 42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
PG P G GP R PLGP
Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...
protein_align_feature table as the following cigar line:
7M4D12M2I2MD7M
=cut
package Bio::EnsEMBL::Utils::Converter::bio_ens_hit;
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;
]]>