Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens_hit =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;