Raw content of Bio::SearchIO::blastxml # $Id: blastxml.pm,v 1.24 2002/10/26 09:32:16 sac Exp $ # # BioPerl module for Bio::SearchIO::blastxml # # Cared for by Jason Stajich <jason@bioperl.org> # # 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::blastxml - A SearchIO implementation of NCBI Blast XML parsing. =head1 SYNOPSIS use Bio::SearchIO; my $searchin = new Bio::SearchIO(-format => 'blastxml', -file => 't/data/plague_yeast.bls.xml'); while( my $result = $searchin->next_result ) { } # one can also request that the parser NOT keep the XML data in memory # by using the tempfile initialization flag. my $searchin = new Bio::SearchIO(-tempfile => 1, -format => 'blastxml', -file => 't/data/plague_yeast.bls.xml'); while( my $result = $searchin->next_result ) { } =head1 DESCRIPTION This object implements a NCBI Blast XML parser. There is one additional initialization flag from the SearchIO defaults - that is the -tempfile flag. If specified as true, then the parser will write out each report to a temporary filehandle rather than holding the entire report as a string in memory. The reason this is done in the first place is NCBI reports have an uncessary E<lt>?xml version="1.0"?E<gt> at the beginning of each report and RPS-BLAST reports have an additional unecessary RPS-BLAST tag at the top of each report. So we currently have implemented the work around by preparsing the file (yes it makes the process slower, but it works). =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/MailList.shtml - About the mailing lists =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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =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::blastxml; use vars qw(@ISA $DTD %MAPPING %MODEMAP $DEBUG); use strict; $DTD = 'ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NCBI_BlastOutput.dtd'; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use Bio::SearchIO; use XML::Parser::PerlSAX; use XML::Handler::Subs; use HTML::Entities; use IO::File; BEGIN { # mapping of NCBI Blast terms to Bioperl hash keys %MODEMAP = ('BlastOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( # 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', # these are ignored for now 'Hsp_num' => 'HSP-order', 'Hsp_pattern-from' => 'patternend', 'Hsp_pattern-to' => 'patternstart', 'Hsp_density' => 'hspdensity', # 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', 'BlastOutput_program' => 'RESULT-algorithm_name', 'BlastOutput_version' => 'RESULT-algorithm_version', 'BlastOutput_query-def' => 'RESULT-query_description', 'BlastOutput_query-len' => 'RESULT-query_length', 'BlastOutput_db' => 'RESULT-database_name', 'BlastOutput_reference' => 'RESULT-program_reference', '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'}, ); eval { require Time::HiRes }; if( $@ ) { $DEBUG = 0; } } @ISA = qw(Bio::SearchIO ); =head2 new Title : new Usage : my $searchio = new Bio::SearchIO(-format => 'blastxml', -file => 'filename', -tempfile => 1); Function: Initializes the object - this is chained through new in SearchIO Returns : Bio::SearchIO::blastxml object Args : One additional argument from the format and file/fh parameters. -tempfile => boolean. Defaults to false. Write out XML data to a temporary filehandle to send to PerlSAX parser. =cut =head2 _initialize Title : _initialize Usage : private Function: Initializes the object - this is chained through new in SearchIO =cut sub _initialize{ my ($self,@args) = @_; $self->SUPER::_initialize(@args); my ($usetempfile) = $self->_rearrange([qw(TEMPFILE)],@args); defined $usetempfile && $self->use_tempfile($usetempfile); $self->{'_xmlparser'} = new XML::Parser::PerlSAX(); $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0); } =head2 next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; my $data = ''; my $firstline = 1; my ($tfh); if( $self->use_tempfile ) { $tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!"); $tfh->autoflush(1); } my $okaytoprocess; while( defined( $_ = $self->_readline) ) { if( /^RPS-BLAST/i ) { $self->{'_type'} = 'RPSBLAST'; next; } if( /^<\?xml version/ && ! $firstline) { $self->_pushback($_); last; } $_ = decode_entities($_); # s/\&apos;/\`/g; # s/\&gt;/\>/g; # s/\&lt;/\</g; $okaytoprocess = 1; if( defined $tfh ) { print $tfh $_; } else { $data .= $_; } $firstline = 0; } return undef unless( $okaytoprocess); my %parser_args; if( defined $tfh ) { seek($tfh,0,0); %parser_args = ('Source' => { 'ByteStream' => $tfh }, 'Handler' => $self); } else { %parser_args = ('Source' => { 'String' => $data }, 'Handler' => $self); } my $result; my $starttime; if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; } eval { $result = $self->{'_xmlparser'}->parse(%parser_args); $self->{'_result_count'}++; }; if( $@ ) { $self->warn("error in parsing a report:\n $@"); $result = undef; } if( $DEBUG ) { $self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime))); } # parsing magic here - but we call event handlers rather than # instantiating things return $result; } =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'}= undef; } =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) = @_; 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($data->{'Attributes'}); } } if($nm eq 'BlastOutput') { $self->{'_values'} = {}; $self->{'_result'}= undef; } } =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( 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( $MAPPING{$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( $nm eq 'Iteration' || $nm eq 'Hit_hsps' || $nm eq 'Parameters' || $nm eq 'BlastOutput_param' || $nm eq 'Iteration_hits' || $nm eq 'Statistics' || $nm eq 'BlastOutput_iterations' ){ } else { $self->debug("ignoring unrecognized element type $nm\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( $nm eq 'BlastOutput' ); return $rc; } =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'}; } =head2 use_tempfile Title : use_tempfile Usage : $obj->use_tempfile($newval) Function: Get/Set boolean flag on whether or not use a tempfile Example : Returns : value of use_tempfile Args : newvalue (optional) =cut sub use_tempfile{ my ($self,$value) = @_; if( defined $value) { $self->{'_use_tempfile'} = $value; } return $self->{'_use_tempfile'}; } sub result_count { my $self = shift; return $self->{'_result_count'}; } 1;