# $Id: BlastHandler.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::SearchIO::XML::BlastHandler # # Please direct questions and support issues to # # Cared for by Jason Stajich, Chris Fields # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing. =head1 SYNOPSIS # This is not to be used directly. =head1 DESCRIPTION This is the XML handler for BLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for Bio::Search object generation. This was recently split off from the original code for Bio::SearchIO::blastxml primarily for maintenance purposes. =head1 DEPENDENCIES In addition to parts of the Bio:: hierarchy, this module uses: XML::SAX::Base which comes with the XML::SAX distribution. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.open-bio.org/ =head1 AUTHOR - Jason Stajich, Chris Fields Email jason-at-bioperl.org Email cjfields-at-uiuc dot edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::XML::BlastHandler; use base qw(Bio::Root::Root XML::SAX::Base); my %MODEMAP = ( 'Iteration' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); # major post 2.2.12 BLAST XML changes # 1) moved XML Handler to it's own class # 2) reconfigure blastxml to deal with old and new BLAST XML output my %MAPPING = ( # Result-specific fields 'BlastOutput_program' => 'RESULT-algorithm_name', 'BlastOutput_version' => 'RESULT-algorithm_version', 'BlastOutput_db' => 'RESULT-database_name', 'BlastOutput_reference' => 'RESULT-program_reference', 'BlastOutput_query-def' => 'RESULT-query_description', 'BlastOutput_query-len' => 'RESULT-query_length', 'BlastOutput_query-ID' => 'runid', 'Parameters_matrix' => { 'RESULT-parameters' => 'matrix'}, 'Parameters_expect' => { 'RESULT-parameters' => 'expect'}, 'Parameters_include' => { 'RESULT-parameters' => 'include'}, 'Parameters_sc-match' => { 'RESULT-parameters' => 'match'}, 'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch'}, 'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen'}, 'Parameters_gap-extend' => { 'RESULT-parameters' => 'gapext'}, 'Parameters_filter' => {'RESULT-parameters' => 'filter'}, 'Statistics_db-num' => 'RESULT-database_entries', 'Statistics_db-len' => 'RESULT-database_letters', 'Statistics_hsp-len' => { 'RESULT-statistics' => 'hsplength'}, 'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace'}, 'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' }, 'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' }, 'Statistics_entropy' => { 'RESULT-statistics' => 'entropy'}, # HSP specific fields 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame'=> 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', # Hit specific fields 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_num' => 'HIT-order', 'Iteration_iter-num' => 'HIT-iteration', 'Iteration_stat' => 'HIT-iteration_statistic', # if these tags are present, they will overwrite the # above with more current data (i.e. multiquery hits) 'Iteration_query-def' => 'RESULT-query_description', 'Iteration_query-len' => 'RESULT-query_length', 'Iteration_query-ID' => 'runid', ); # these XML tags are ignored for now my %IGNOREDTAGS = ( 'Hsp_num' => 1,#'HSP-order', 'Hsp_pattern-from' => 1,#'patternend', 'Hsp_pattern-to' => 1,#'patternstart', 'Hsp_density' => 1,#'hspdensity', 'Iteration_message' => 1, 'Hit_hsps' => 1, 'BlastOutput_param' => 1, 'Iteration_hits' => 1, 'Statistics' => 1, 'Parameters' => 1, 'BlastOutput' => 1, 'BlastOutput_iterations' => 1, ); =head2 SAX methods =cut =head2 start_document Title : start_document Usage : $parser->start_document; Function: SAX method to indicate starting to parse a new document Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= []; } =head2 end_document Title : end_document Usage : $parser->end_document; Function: SAX method to indicate finishing parsing a new document Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; # reset data carried throughout parse $self->{'_resultdata'} = undef; # pass back ref to results queue; caller must reset handler results queue return $self->{'_result'}; } =head2 start_element Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { if( $self->eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->eventHandler->$func($data->{'Attributes'}); } } } =head2 end_element Title : end_element Usage : $parser->end_element($data) Function: Signals finishing an element Returns : Bio::Search object dpending on what type of element Args : hash ref for data =cut sub end_element{ my ($self,$data) = @_; my $nm = $data->{'Name'}; my $rc; if($nm eq 'BlastOutput_program' && $self->{'_last_data'} =~ /(t?blast[npx])/i ) { $self->{'_type'} = uc $1; } if ($nm eq 'Iteration') { map { $self->{'_values'}->{$_} = $self->{'_resultdata'}->{$_}; } keys %{ $self->{'_resultdata'} }; } if( my $type = $MODEMAP{$nm} ) { if( $self->eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->eventHandler->$func($self->{'_type'}, $self->{'_values'}); } } elsif( exists $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } elsif( exists $IGNOREDTAGS{$nm} ){ # ignores these elements for now } else { $self->debug("ignoring unrecognized element type $nm\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element # add to ResultI array $self->{'_result'} = $rc if( $nm eq 'Iteration' ); # reset values for each Result round if ($nm eq 'Iteration') { $self->{'_values'} = {}; } } =head2 characters Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data' =cut sub characters{ my ($self,$data) = @_; return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ ); $self->{'_last_data'} .= $data->{'Data'}; } sub eventHandler { my $self = shift; return $self->{'_handler'} = shift if @_; return $self->{'_handler'}; } 1;