bio_ens_hit documentation.

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

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_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 _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);

}

  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

_bio_ens_seqFeature_converter	No description	Code
_convert_single	No description	Code
_convert_single_hit	No description	Code
_convert_single_hsp	No description	Code
_initialize	No description	Code