Raw content of Bio::SearchIO::fasta # $Id: fasta.pm,v 1.33.2.3 2003/08/28 16:01:03 jason Exp $ # # BioPerl module for Bio::SearchIO::fasta # # 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::fasta - A SearchIO parser for FASTA results =head1 SYNOPSIS # Do not use this object directly, use it through the SearchIO system use Bio::SearchIO; my $searchio = new Bio::SearchIO(-format => 'fasta', -file => 'report.FASTA'); while( my $result = $searchio->next_result ) { # .... } =head1 DESCRIPTION This object contains the event based parsing code for FASTA format reports. =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::fasta; use vars qw(@ISA %MODEMAP %MAPPING $IDLENGTH); use strict; # Object preamble - inherits from Bio::Root::RootI use Bio::SearchIO; use POSIX; BEGIN { # Set IDLENGTH to a new value if you have # compile FASTA with a different ID length # (actually newest FASTA allows the setting of this # via -C parameter, default is 6) $IDLENGTH = 6; # mapping of NCBI Blast terms to Bioperl hash keys %MODEMAP = ('FastaOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); # This should really be done more intelligently, like with # XSLT %MAPPING = ( 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_sw-score' => 'HSP-swscore', '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-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_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'FastaOutput_program' => 'RESULT-algorithm_name', 'FastaOutput_version' => 'RESULT-algorithm_version', 'FastaOutput_query-def'=> 'RESULT-query_name', 'FastaOutput_querydesc'=> 'RESULT-query_description', 'FastaOutput_query-len'=> 'RESULT-query_length', 'FastaOutput_db' => 'RESULT-database_name', 'FastaOutput_db-len' => 'RESULT-database_entries', 'FastaOutput_db-let' => 'RESULT-database_letters', '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-ext' => { 'RESULT-parameters' => 'gapext'}, 'Parameters_word-size' => { 'RESULT-parameters' => 'wordsize'}, 'Parameters_ktup' => { 'RESULT-parameters' => 'ktup'}, 'Parameters_filter' => {'RESULT-parameters' => 'filter'}, 'Statistics_db-num' => { 'RESULT-statistics' => 'dbentries'}, 'Statistics_db-len' => { 'RESULT-statistics' => 'dbletters'}, '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'}, ); } @ISA = qw(Bio::SearchIO ); =head2 new Title : new Usage : my $obj = new Bio::SearchIO::fasta(); Function: Builds a new Bio::SearchIO::fasta object Returns : Bio::SearchIO::fasta Args : -idlength - set ID length to something other than the default (7), this is only necessary if you have compiled FASTA with a new default id length to display in the HSP alignment blocks =cut sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); return unless @args; my ($idlength) = $self->_rearrange([qw(IDLENGTH)],@args); $self->idlength($idlength || $IDLENGTH); $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::FastaHSP')); return 1; } =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 $seentop = 0; my $current_hsp; $self->start_document(); my @hit_signifs; while( defined ($_ = $self->_readline )) { next if( ! $self->in_element('hsp') && /^\s+$/); # skip empty lines if( /(\S+)\s+searches\s+a\s+((protein\s+or\s+DNA\s+sequence)|(sequence\s+database))/i || /(\S+) compares a/ || ( m/^# / && ($_ = $self->_readline) && /(\S+)\s+searches\s+a\s+((protein\s+or\s+DNA\s+sequence)|(sequence\s+database))/i || /(\S+) compares a/ ) ) { if( $seentop ) { $self->_pushback($_); $self->end_element({ 'Name' => 'FastaOutput'}); return $self->end_document(); } $self->{'_reporttype'} = $1; $self->start_element({ 'Name' => 'FastaOutput' } ); $self->{'_result_count'}++; $seentop = 1; $self->element({ 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'}}); $_ = $self->_readline(); my ($version) = (/version\s+(\S+)/); $version = '' unless defined $version; $self->{'_version'} = $version; $self->element({ 'Name' => 'FastaOutput_version', 'Data' => $version}); my ($last, $leadin, $type, $querylen, $querytype, $querydef); while( defined($_ = $self->_readline()) ) { if( /^ ( (?:\s+>) | # fa33 lead-in (?:\s*\d+\s*>>>) # fa34 mlib lead-in ) (.*) /x ) { ($leadin, $querydef) = ($1, $2); if ($leadin =~ m/>>>/) { if($querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt)\s*$/o ) { ($querydef, $querylen, $querytype) = ($1, $2, $3); last; } } else { if( $last =~ /(\S+)[:,]\s*(\d+)\s+(aa|nt)/ ) { ($querylen, $querytype) = ($2, $3); $querydef ||= $1; last; } } } elsif ( m/^\s*vs\s+\S+/o ) { if ( $last =~ /(\S+)[,:]\s+(\d+)\s+(aa|nt)/o) { ($querydef, $querylen, $querytype) = ($1, $2, $3); last; } } $last = $_; } if( $self->{'_reporttype'} && $self->{'_reporttype'} eq 'FASTA' ) { if( $querytype eq 'nt') { $self->{'_reporttype'} = 'FASTN' ; } elsif( $querytype eq 'aa' ) { $self->{'_reporttype'} = 'FASTP' ; } } my ($name, $descr) = $querydef =~ m/^(\S+)\s*(.*?)\s*$/o; $self->element({'Name' => 'FastaOutput_query-def', 'Data' => $name}); $self->element({'Name' => 'FastaOutput_querydesc', 'Data' => $descr}); if ($querylen) { $self->element({'Name' => 'FastaOutput_query-len', 'Data' => $querylen}); } else { $self->warn("unable to find and set query length"); } if( $last =~ /^\s*vs\s+(\S+)/ || ($last =~ /^searching\s+(\S+)\s+library/) || (defined $_ && /^\s*vs\s+(\S+)/) || (defined ($_ = $self->_readline()) && /^\s*vs\s+(\S+)/) ) { $self->element({'Name' => 'FastaOutput_db', 'Data' => $1}); } elsif (m/^\s+opt(?:\s+E\(\))?$/o) { # histogram ... read over it more rapidly than the larger outer loop: while (defined($_ = $self->_readline)) { last if m/^>\d+/; } } } elsif( /(\d+) residues in\s+(\d+)\s+sequences/ ) { $self->element({'Name' => 'FastaOutput_db-let', 'Data' => $1}); $self->element({'Name' => 'FastaOutput_db-len', 'Data' => $2}); $self->element({'Name' => 'Statistics_db-len', 'Data' => $1}); $self->element({'Name' => 'Statistics_db-num', 'Data' => $2}); } elsif( /Lambda=\s*(\S+)/ ) { $self->element({'Name' => 'Statistics_lambda', 'Data' => $1}); } elsif (/K=\s*(\S+)/) { $self->element({'Name' => 'Statistics_kappa', 'Data' => $1}); } elsif( /^\s*(Smith-Waterman).+(\S+)\s*matrix [^\]]*?(xS)?\]/ ) { $self->element({'Name' => 'Parameters_matrix', 'Data' => $2}); $self->element({'Name' => 'Parameters_filter', 'Data' => defined $3 ? 1 : 0, }); $self->{'_reporttype'} = $1; $self->element({ 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'}}); } elsif( /The best( related| unrelated)? scores are:/ ) { my $rel = $1; my @labels = split; @labels = map { if ($_ =~ m/^E\((\d+)\)$/o) { $self->element({'Name' => 'Statistics_eff-space', 'Data' => $1}); "evalue"; } else { $_; } } @labels[$rel ? 5 : 4 .. $#labels]; while( defined ($_ = $self->_readline() ) && ! /^\s+$/ ) { my @line = split; if ($line[-1] =~ m/\=/o && $labels[-1] eq 'fs') { # unlabelled alignment hit; push @labels, "aln_code"; } my %data; @data{@labels} = splice(@line, @line - @labels); if ($line[-1] =~ m/\[([1-6rf])\]/o) { my $fr = $1; $data{lframe} = ($fr =~ /\d/o ? ($fr <= 3 ? "+$fr" : "-@{[$fr-3]}") : ($fr eq 'f' ? '+1' : '-1') ); pop @line; } else { $data{lframe} = '0'; } if ($line[-1] =~ m/^\(?(\d+)\)$/) { $data{hit_len} = $1; pop @line; if ($line[-1] =~ m/^\($/) { pop @line; } } else { $data{hit_len} = 0; } # rebuild the first part of the line, preserving spaces: ($_) = m/^(\S+(?:\s+\S+){$#line})/; my ($id, $desc) = split(/\s+/,$_,2); my @pieces = split(/\|/,$id); my $acc = pop @pieces; $acc =~ s/\.\d+$//; @data{qw(id desc acc)} = ($id, $desc, $acc); push @hit_signifs, \%data; } } elsif( /^\s*([T]?FAST[XYAF]).+,\s*(\S+)\s*matrix[^\]]+?(xS)?\]\s*ktup:\s*(\d+)/ ) { $self->element({'Name' => 'Parameters_matrix', 'Data' => $2}); $self->element({'Name' => 'Parameters_filter', 'Data' => defined $3 ? 1 : 0, }); $self->element({'Name' => 'Parameters_ktup', 'Data' => $4}); $self->{'_reporttype'} = $1 if( $self->{'_reporttype'} !~ /FAST[PN]/i ) ; $self->element({ 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'}}); } elsif( /(?:gap\-pen|open\/ext):\s+([\-\+]?\d+)\s*\/\s*([\-\+]?\d+).+width:\s+(\d+)/ ) { $self->element({'Name' => 'Parameters_gap-open', 'Data' => $1}); $self->element({'Name' => 'Parameters_gap-ext', 'Data' => $2}); $self->element({'Name' => 'Parameters_word-size', 'Data' => $3}); } elsif( /^>>(.+?)\s+\((\d+)\s*(aa|nt)\)$/ ) { if( $self->in_element('hsp') ) { $self->end_element({ 'Name' => 'Hsp'}); } if( $self->in_element('hit') ) { $self->end_element({ 'Name' => 'Hit'}); } $self->start_element({'Name' => 'Hit'}); $self->element({ 'Name' => 'Hit_len', 'Data' => $2}); my ($id,$desc) = split(/\s+/,$1,2); $self->element({ 'Name' => 'Hit_id', 'Data' => $id}); my @pieces = split(/\|/,$id); my $acc = pop @pieces; $acc =~ s/\.\d+$//; $self->element({ 'Name' => 'Hit_accession', 'Data' => $acc}); $self->element({ 'Name' => 'Hit_def', 'Data' => $desc}); $_ = $self->_readline(); my ($score,$bits,$e) = /Z-score: \s* (\S+) \s* (?: bits: \s* (\S+) \s+ )? (?: E|expect ) \s* \(\) :? \s*(\S+)/x; $bits = $score unless defined $bits; my $v = shift @hit_signifs; if( defined $v ) { @{$v}{qw(evalue bits z-sc)} = ($e, $bits, $score); } $self->element({'Name' => 'Hit_signif', 'Data' => $v ? $v->{evalue} : $e }); $self->element({'Name' => 'Hit_score', 'Data' => $v ? $v->{bits} : $bits }); $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_score', 'Data' => $v ? $v->{'z-sc'} : $score }); $self->element({'Name' => 'Hsp_evalue', 'Data' => $v ? $v->{evalue} : $e }); $self->element({'Name' => 'Hsp_bit-score', 'Data' => $v ? $v->{bits} : $bits }); $_ = $self->_readline(); if( /Smith-Waterman score:\s*(\d+)/ ) { $self->element({'Name' => 'Hsp_sw-score', 'Data' => $1}); } if( / (\S+)\% \s* identity (?:\s* \( \s* (\S+)\% \s* ungapped \) )? \s* in \s* (\d+) \s+ (?:aa|nt) \s+ overlap \s* \( (\d+) \- (\d+) : (\d+) \- (\d+) \) /x ) { my ($identper,$gapper,$len,$querystart, $queryend,$hitstart,$hitend) = ($1,$2,$3,$4,$5,$6,$7); my $ident = POSIX::ceil(($identper/100) * $len); my $gaps = ( defined $gapper ) ? POSIX::ceil ( ($gapper/100) * $len) : undef; $self->element({'Name' => 'Hsp_gaps', 'Data' => $gaps}); $self->element({'Name' => 'Hsp_identity', 'Data' => $ident}); $self->element({'Name' => 'Hsp_positive', 'Data' => $ident}); $self->element({'Name' => 'Hsp_align-len', 'Data' => $len}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $querystart}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $queryend}); $self->element({'Name' => 'Hsp_hit-from', 'Data' => $hitstart}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $hitend}); } if ($v) { $self->element({'Name' => 'Hsp_querygaps', 'Data' => $v->{qgaps} }) if exists $v->{qgaps}; $self->element({'Name' => 'Hsp_hitgaps', 'Data' => $v->{lgaps} }) if exists $v->{lgaps}; if ($self->{'_reporttype'} =~ m/^FAST[NXY]$/o) { if( 8 == scalar grep { exists $v->{$_} } qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) ) { if ($v->{ax0} < $v->{an0}) { $self->element({'Name' => 'Hsp_query-frame', 'Data' => "-@{[(($v->{px0} - $v->{ax0}) % 3) + 1]}" }); } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => "+@{[(($v->{an0} - $v->{pn0}) % 3) + 1]}" }); } if ($v->{ax1} < $v->{an1}) { $self->element({'Name' => 'Hsp_hit-frame', 'Data' => "-@{[(($v->{px1} - $v->{ax1}) % 3) + 1]}" }); } else { $self->element({'Name' => 'Hsp_hit-frame', 'Data' => "+@{[(($v->{an1} - $v->{pn1}) % 3) + 1]}" }); } } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => $v->{lframe} }); $self->element({'Name' => 'Hsp_hit-frame', 'Data' => 0 }); } } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => 0 }); $self->element({'Name' => 'Hsp_hit-frame', 'Data' => $v->{lframe} }); } } else { $self->warn( "unable to parse FASTA score line: $_"); } } elsif( /\d+\s*residues\s*in\s*\d+\s*query\s*sequences/ ) { if( $self->in_element('hsp') ) { $self->end_element({'Name' => 'Hsp'}); } if( $self->in_element('hit') ) { $self->end_element({'Name' => 'Hit'}); } # $_ = $self->_readline(); # my ( $liblen,$libsize) = /(\d+)\s+residues\s*in(\d+)\s*library/; # fast forward to the end of the file as there is # nothing else left to do with this file and want to be sure and # reset it while(defined($_ = $self->_readline() ) ) { last if( /^Function used was/); if( /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+sequence)|(sequence\s+database)/ ) { $self->_pushback($_); } } if (@hit_signifs) { # process remaining best hits for my $h (@hit_signifs) { # Hsp_score Hsp_evalue Hsp_bit-score # Hsp_sw-score Hsp_gaps Hsp_identity Hsp_positive # Hsp_align-len Hsp_query-from Hsp_query-to # Hsp_hit-from Hsp_hit-to Hsp_qseq Hsp_midline $self->start_element({'Name' => 'Hit'}); $self->element({ 'Name' => 'Hit_len', 'Data' => $h->{hit_len} }) if exists $h->{hit_len}; $self->element({ 'Name' => 'Hit_id', 'Data' => $h->{id} }) if exists $h->{id}; $self->element({ 'Name' => 'Hit_accession', 'Data' => $h->{acc} }) if exists $h->{acc}; $self->element({ 'Name' => 'Hit_def', 'Data' => $h->{desc} }) if exists $h->{desc}; $self->element({'Name' => 'Hit_signif', 'Data' => $h->{evalue} }) if exists $h->{evalue}; $self->element({'Name' => 'Hit_score', 'Data' => $h->{bits} }) if exists $h->{bits}; $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_score', 'Data' => $h->{'z-sc'} }) if exists $h->{'z-sc'}; $self->element({'Name' => 'Hsp_evalue', 'Data' => $h->{evalue} }) if exists $h->{evalue}; $self->element({'Name' => 'Hsp_bit-score', 'Data' => $h->{bits} }) if exists $h->{bits}; $self->element({'Name' => 'Hsp_sw-score', 'Data' => $h->{sw} }) if exists $h->{sw}; $self->element({'Name' => 'Hsp_gaps', 'Data' => $h->{'%_gid'} }) if exists $h->{'%_gid'}; $self->element({'Name' => 'Hsp_identity', 'Data' => POSIX::ceil($h->{'%_id'} * $h->{alen}) }) if (exists $h->{'%_id'} && exists $h->{alen}); $self->element({'Name' => 'Hsp_positive', 'Data' => 100 * $h->{'%_id'} }) if exists $h->{'%_id'}; $self->element({'Name' => 'Hsp_align-len', 'Data' => $h->{alen} }) if exists $h->{alen}; $self->element({'Name' => 'Hsp_query-from', 'Data' => $h->{an0} }) if exists $h->{an0}; $self->element({'Name' => 'Hsp_query-to', 'Data' => $h->{ax0} }) if exists $h->{ax0}; $self->element({'Name' => 'Hsp_hit-from', 'Data' => $h->{an1} }) if exists $h->{an1}; $self->element({'Name' => 'Hsp_hit-to', 'Data' => $h->{ax1} }) if exists $h->{ax1}; $self->element({'Name' => 'Hsp_querygaps', 'Data' => $h->{qgaps} }) if exists $h->{qgaps}; $self->element({'Name' => 'Hsp_hitgaps', 'Data' => $h->{lgaps} }) if exists $h->{lgaps}; if ($self->{'_reporttype'} =~ m/^FAST[NXY]$/o) { if( 8 == scalar grep { exists $h->{$_} } qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) ) { if ($h->{ax0} < $h->{an0}) { $self->element({'Name' => 'Hsp_query-frame', 'Data' => "-@{[(($h->{px0} - $h->{ax0}) % 3) + 1]}" }); } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => "+@{[(($h->{an0} - $h->{pn0}) % 3) + 1]}" }); } if ($h->{ax1} < $h->{an1}) { $self->element({'Name' => 'Hsp_hit-frame', 'Data' => "-@{[(($h->{px1} - $h->{ax1}) % 3) + 1]}" }); } else { $self->element({'Name' => 'Hsp_hit-frame', 'Data' => "+@{[(($h->{an1} - $h->{pn1}) % 3) + 1]}" }); } } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => $h->{lframe} }); $self->element({'Name' => 'Hsp_hit-frame', 'Data' => 0 }); } } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => 0 }); $self->element({'Name' => 'Hsp_hit-frame', 'Data' => $h->{lframe} }); } $self->end_element({'Name' => 'Hsp'}); $self->end_element({'Name' => 'Hit'}); } } $self->end_element({ 'Name' => 'FastaOutput'}); return $self->end_document(); } elsif( /^\s*\d+\s*>>>/) { if ($self->within_element('FastaOutput')) { if( $self->in_element('hsp') ) { $self->end_element({'Name' => 'Hsp'}); } if( $self->in_element('hit') ) { $self->end_element({'Name' => 'Hit'}); } if (@hit_signifs) { # process remaining best hits for my $h (@hit_signifs) { $self->start_element({'Name' => 'Hit'}); $self->element({ 'Name' => 'Hit_len', 'Data' => $h->{hit_len} }) if exists $h->{hit_len}; $self->element({ 'Name' => 'Hit_id', 'Data' => $h->{id} }) if exists $h->{id}; $self->element({ 'Name' => 'Hit_accession', 'Data' => $h->{acc} }) if exists $h->{acc}; $self->element({ 'Name' => 'Hit_def', 'Data' => $h->{desc} }) if exists $h->{desc}; $self->element({'Name' => 'Hit_signif', 'Data' => $h->{evalue} }) if exists $h->{evalue}; $self->element({'Name' => 'Hit_score', 'Data' => $h->{bits} }) if exists $h->{bits}; $self->start_element({'Name' => 'Hsp'}); $self->element({'Name' => 'Hsp_score', 'Data' => $h->{'z-sc'} }) if exists $h->{'z-sc'}; $self->element({'Name' => 'Hsp_evalue', 'Data' => $h->{evalue} }) if exists $h->{evalue}; $self->element({'Name' => 'Hsp_bit-score', 'Data' => $h->{bits} }) if exists $h->{bits}; $self->element({'Name' => 'Hsp_sw-score', 'Data' => $h->{sw} }) if exists $h->{sw}; $self->element({'Name' => 'Hsp_gaps', 'Data' => $h->{'%_gid'} }) if exists $h->{'%_gid'}; $self->element({'Name' => 'Hsp_identity', 'Data' => POSIX::ceil($h->{'%_id'} * $h->{alen}) }) if (exists $h->{'%_id'} && exists $h->{alen}); $self->element({'Name' => 'Hsp_positive', 'Data' => $h->{'%_id'} }) if exists $h->{'%_id'}; $self->element({'Name' => 'Hsp_align-len', 'Data' => $h->{alen} }) if exists $h->{alen}; $self->element({'Name' => 'Hsp_query-from', 'Data' => $h->{an0} }) if exists $h->{an0}; $self->element({'Name' => 'Hsp_query-to', 'Data' => $h->{ax0} }) if exists $h->{ax0}; $self->element({'Name' => 'Hsp_hit-from', 'Data' => $h->{an1} }) if exists $h->{an1}; $self->element({'Name' => 'Hsp_hit-to', 'Data' => $h->{ax1} }) if exists $h->{ax1}; $self->element({'Name' => 'Hsp_querygaps', 'Data' => $h->{qgaps} }) if exists $h->{qgaps}; $self->element({'Name' => 'Hsp_hitgaps', 'Data' => $h->{lgaps} }) if exists $h->{lgaps}; if ($self->{'_reporttype'} =~ m/^FAST[NXY]$/o) { if( 8 == scalar grep { exists $h->{$_} } qw(an0 ax0 pn0 px0 an1 ax1 pn1 px1) ) { if ($h->{ax0} < $h->{an0}) { $self->element({'Name' => 'Hsp_query-frame', 'Data' => "-@{[(($h->{px0} - $h->{ax0}) % 3) + 1]}" }); } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => "+@{[(($h->{an0} - $h->{pn0}) % 3) + 1]}" }); } if ($h->{ax1} < $h->{an1}) { $self->element({'Name' => 'Hsp_hit-frame', 'Data' => "-@{[(($h->{px1} - $h->{ax1}) % 3) + 1]}" }); } else { $self->element({'Name' => 'Hsp_hit-frame', 'Data' => "+@{[(($h->{an1} - $h->{pn1}) % 3) + 1]}" }); } } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => $h->{lframe} }); $self->element({'Name' => 'Hsp_hit-frame', 'Data' => 0 }); } } else { $self->element({'Name' => 'Hsp_query-frame', 'Data' => 0 }); $self->element({'Name' => 'Hsp_hit-frame', 'Data' => $h->{lframe} }); } $self->end_element({'Name' => 'Hsp'}); $self->end_element({'Name' => 'Hit'}); } } $self->end_element({ 'Name' => 'FastaOutput' }); $self->_pushback($_); return $self->end_document(); } else { $self->start_element({ 'Name' => 'FastaOutput' }); $self->{'_result_count'}++; $seentop = 1; $self->element({ 'Name' => 'FastaOutput_program', 'Data' => $self->{'_reporttype'} }); $self->element({ 'Name' => 'FastaOutput_version', 'Data' => $self->{'_version'} }); my ($type, $querylen, $querytype, $querydef); if( /^\s*\d+\s*>>>(.*)/ ) { $querydef = $1; if($querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt)\s*$/o ) { ($querydef, $querylen, $querytype) = ($1, $2, $3); } } if( $self->{'_reporttype'} && $self->{'_reporttype'} eq 'FASTA' ) { if( $querytype eq 'nt') { $self->{'_reporttype'} = 'FASTN' ; } elsif( $querytype eq 'aa' ) { $self->{'_reporttype'} = 'FASTP' ; } } my ($name,$descr) = ($querydef =~ m/^(\S+)(?:\s+(.*))?\s*$/o); $self->element({'Name' => 'FastaOutput_query-def', 'Data' => $name}); $self->element({'Name' => 'FastaOutput_querydesc', 'Data' => $descr}); if ($querylen) { $self->element({'Name' => 'FastaOutput_query-len', 'Data' => $querylen}); } else { $self->warn("unable to find and set query length"); } if( defined ($_ = $self->_readline()) && /^\s*vs\s+(\S+)/ ) { $self->element({'Name' => 'FastaOutput_db', 'Data' => $1}); } } } elsif( $self->in_element('hsp' ) ) { my @data = ( '','',''); my $count = 0; my $len = $self->idlength + 1; my ($seq1_id); while( defined($_ ) ) { chomp; $self->debug( "$count $_\n"); if( /residues in \d+\s+query\s+sequences/) { $self->_pushback($_); last; } elsif( /^>>/ ) { $self->_pushback($_); last; } elsif (/^\s*\d+\s*>>>/) { $self->_pushback($_); last; } if( $count == 0 ) { unless( /^\s+\d+/ || /^\s+$/) { $self->_pushback($_); $count = 2; } } elsif( $count == 1 || $count == 3 ) { if( /^(\S+)\s+/ ) { $len = CORE::length($1) if $len < CORE::length($1); s/\s+$//; # trim trailing spaces,we don't want them $data[$count-1] = substr($_,$len); } elsif( /^\s+(\d+)/ ) { $count = -1; $self->_pushback($_); } elsif( /^\s+$/ || length($_) == 0) { $count = 5; # going to skip these } else { $self->warn("Unrecognized alignment line ($count) '$_'"); } } elsif( $count == 2 ) { if( /^\s+\d+\s+/ ) { $self->warn("$_\n"); $count = 4; } else { # toss the first IDLENGTH characters of the line if( length($_) >= $len ) { $data[$count-1] = substr($_,$len); } } } last if( $count++ >= 5); $_ = $self->_readline(); } if( length($data[0]) > 0 || length($data[2]) > 0 ) { $self->characters({'Name' => 'Hsp_qseq', 'Data' => $data[0] }); $self->characters({'Name' => 'Hsp_midline', 'Data' => $data[1]}); $self->characters({'Name' => 'Hsp_hseq', 'Data' => $data[2]}); } } else { if( ! $seentop ) { $self->debug($_); $self->warn("unrecognized FASTA Family report file!"); return undef; } } } } =head2 start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub start_element{ my ($self,$data) = @_; # we currently don't care about attributes my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; } if($nm eq 'FastaOutput') { $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; } } =head2 end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' =cut sub end_element { my ($self,$data) = @_; my $nm = $data->{'Name'}; my $rc; # Hsp are sort of weird, in that they end when another # object begins so have to detect this in end_element for now if( $nm eq 'Hsp' ) { foreach ( qw(Hsp_qseq Hsp_midline Hsp_hseq) ) { $self->element({'Name' => $_, 'Data' => $self->{'_last_hspdata'}->{$_}}); } $self->{'_last_hspdata'} = {} } if( my $type = $MODEMAP{$nm} ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } 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'}; } } else { $self->warn( "unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at # end of an element $self->{'_result'} = $rc if( $nm eq 'FastaOutput' ); return $rc; } =head2 element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' =cut sub element{ my ($self,$data) = @_; $self->start_element($data); $self->characters($data); $self->end_element($data); } =head2 characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string =cut sub characters{ my ($self,$data) = @_; return unless ( defined $data->{'Data'} ); if( $data->{'Data'} =~ /^\s+$/ ) { return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/; } if( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'}; } $self->{'_last_data'} = $data->{'Data'}; } =head2 _mode Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional) =cut sub _mode{ my ($self,$value) = @_; if( defined $value) { $self->{'_mode'} = $value; } return $self->{'_mode'}; } =head2 within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub within_element{ my ($self,$name) = @_; return 0 if ( ! defined $name && ! defined $self->{'_elements'} || scalar @{$self->{'_elements'}} == 0) ; foreach ( @{$self->{'_elements'}} ) { if( $_ eq $name || $_ eq $MODEMAP{$name} ) { return 1; } } return 0; } =head2 in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name =cut sub in_element{ my ($self,$name) = @_; return 0 if ! defined $self->{'_elements'}->[0]; return ( $self->{'_elements'}->[0] eq $name || (exists $MODEMAP{$name} && $self->{'_elements'}->[0] eq $MODEMAP{$name}) ); } =head2 start_document Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none =cut sub start_document{ my ($self) = @_; $self->{'_lasttype'} = ''; $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; $self->{'_elements'} = []; } =head2 end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none =cut sub end_document{ my ($self,@args) = @_; return $self->{'_result'}; } =head2 idlength Title : idlength Usage : $obj->idlength($newval) Function: Internal storage of the length of the ID desc in the HSP alignment blocks. Defaults to $IDLENGTH class variable value Returns : value of idlength Args : newvalue (optional) =cut sub idlength{ my ($self,$value) = @_; if( defined $value) { $self->{'_idlength'} = $value; } return $self->{'_idlength'} || $IDLENGTH; } =head2 result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none =cut sub result_count { my $self = shift; return $self->{'_result_count'}; } 1;