Bio::SearchIO blast
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Summary
Bio::SearchIO::blast - Event generator for event based parsing of blast reports
Package variables
No package variables defined.
Included modules
Bio::SearchIO
Inherit
Bio::SearchIO
Synopsis
   # Do not use this object directly - it is used as part of the
# Bio::SearchIO system.
use Bio::SearchIO; my $searchio = new Bio::SearchIO(-format => 'blast', -file => 't/data/ecolitst.bls'); while( my $result = $searchio->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { # ... } } }
Description
This object encapsulated the necessary methods for generating events
suitable for building Bio::Search objects from a BLAST report file.
Read the Bio::SearchIO for more information about how to use this.
Methods
BEGIN Code
charactersDescriptionCode
elementDescriptionCode
end_documentDescriptionCode
end_elementDescriptionCode
in_elementDescriptionCode
next_resultDescriptionCode
result_count
No description
Code
start_documentDescriptionCode
start_elementDescriptionCode
within_elementDescriptionCode
write_result
No description
Code
Methods description
characterscode    nextTop
 Title   : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
elementcodeprevnextTop
 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'
end_documentcodeprevnextTop
 Title   : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
end_elementcodeprevnextTop
 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'
in_elementcodeprevnextTop
 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
next_resultcodeprevnextTop
 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
start_documentcodeprevnextTop
 Title   : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
start_elementcodeprevnextTop
 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'
within_elementcodeprevnextTop
 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
Methods code
BEGINTop
BEGIN {
     # mapping of NCBI Blast terms to Bioperl hash keys
%MODEMAP = ('BlastOutput' => '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_evalue' => 'HSP-evalue', 'Hsp_pvalue' => 'HSP-pvalue', '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', 'Iteration_iter-num' => 'HIT-iteration', 'BlastOutput_program' => 'RESULT-algorithm_name', 'BlastOutput_version' => 'RESULT-algorithm_version', 'BlastOutput_query-def'=> 'RESULT-query_name', 'BlastOutput_query-len'=> 'RESULT-query_length', 'BlastOutput_query-acc'=> 'RESULT-query_accession', 'BlastOutput_querydesc'=> 'RESULT-query_description', 'BlastOutput_db' => 'RESULT-database_name', 'BlastOutput_db-len' => 'RESULT-database_entries', 'BlastOutput_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-extend'=> { 'RESULT-parameters' => 'gapext'}, 'Parameters_filter' => {'RESULT-parameters' => 'filter'}, 'Parameters_allowgaps' => { 'RESULT-parameters' => 'allowgaps'}, 'Statistics_db-len' => {'RESULT-statistics' => 'dbentries'}, 'Statistics_db-let' => { 'RESULT-statistics' => 'dbletters'}, 'Statistics_hsp-len' => { 'RESULT-statistics' => 'effective_hsplength'}, 'Statistics_query-len' => { 'RESULT-statistics' => 'querylength'}, 'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace'}, 'Statistics_eff-spaceused' => { 'RESULT-statistics' => 'effectivespaceused'}, 'Statistics_eff-dblen' => { 'RESULT-statistics' => 'effectivedblength'}, 'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' }, 'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' }, 'Statistics_entropy' => { 'RESULT-statistics' => 'entropy'}, 'Statistics_framewindow'=> { 'RESULT-statistics' => 'frameshiftwindow'}, 'Statistics_decay'=> { 'RESULT-statistics' => 'decayconst'}, 'Statistics_T'=> { 'RESULT-statistics' => 'T'}, 'Statistics_A'=> { 'RESULT-statistics' => 'A'}, 'Statistics_X1'=> { 'RESULT-statistics' => 'X1'}, 'Statistics_X2'=> { 'RESULT-statistics' => 'X2'}, 'Statistics_S1'=> { 'RESULT-statistics' => 'S1'}, 'Statistics_S2'=> { 'RESULT-statistics' => 'S2'}, 'Statistics_hit_to_db' => { 'RESULT-statistics' => 'Hits_to_DB'}, 'Statistics_num_extensions' => { 'RESULT-statistics' => 'num_extensions'}, 'Statistics_num_extensions' => { 'RESULT-statistics' => 'num_extensions'}, 'Statistics_num_suc_extensions' => { 'RESULT-statistics' => 'num_successful_extensions'}, 'Statistics_seqs_better_than_cutoff' => { 'RESULT-statistics' => 'seqs_better_than_cutoff'}, 'Statistics_posted_date' => { 'RESULT-statistics' => 'posted_date'}, # WU-BLAST stats
'Statistics_DFA_states'=> { 'RESULT-statistics' => 'num_dfa_states'}, 'Statistics_DFA_size'=> { 'RESULT-statistics' => 'dfa_size'}, 'Statistics_search_cputime' => { 'RESULT-statistics' => 'search_cputime'}, 'Statistics_total_cputime' => { 'RESULT-statistics' => 'total_cputime'}, 'Statistics_search_actualtime' => { 'RESULT-statistics' => 'search_actualtime'}, 'Statistics_total_actualtime' => { 'RESULT-statistics' => 'total_actualtime'}, 'Statistics_noprocessors' => { 'RESULT-statistics' => 'no_of_processors'}, 'Statistics_neighbortime' => { 'RESULT-statistics' => 'neighborhood_generate_time'}, 'Statistics_starttime' => { 'RESULT-statistics' => 'start_time'}, 'Statistics_endtime' => { 'RESULT-statistics' => 'end_time'}, ); $DEFAULT_BLAST_WRITER_CLASS = 'Bio::Search::Writer::HitTableWriter';
}
charactersdescriptionprevnextTop
sub characters {
   my ($self,$data) = @_;   
   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );   

   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }   
   $self->{'_last_data'} = $data->{'Data'};
}
elementdescriptionprevnextTop
sub element {
   my ($self,$data) = @_;
   $self->start_element($data);       
   $self->characters($data);
   $self->end_element($data);
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   return $self->{'_result'};
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    my $rc;
    if($nm eq 'BlastOutput_program' &&
       $self->{'_last_data'} =~ /(t?blast[npx])/i ) {
	$self->{'_reporttype'} = uc $1; 	    
    }   

    # 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'} = {}; $self->element({'Name' => 'Hsp_query-from', 'Data' => $self->{'_Query'}->{'begin'}}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $self->{'_Query'}->{'end'}}); $self->element({'Name' => 'Hsp_hit-from', 'Data' => $self->{'_Sbjct'}->{'begin'}}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $self->{'_Sbjct'}->{'end'}}); } if( $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 ) { # this is where we shove in the data from the
# hashref info about params or statistics
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->debug( "unknown nm $nm, ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if( defined $type && $type eq 'result' ); return $rc;
}
in_elementdescriptionprevnextTop
sub in_element {
   my ($self,$name) = @_;  
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}
next_resultdescriptionprevnextTop
sub next_result {
   my ($self) = @_;
   
   my $data = '';
   my $seentop = 0;
   my ($reporttype,$seenquery,$reportline);
   $self->start_document();
   my @hit_signifs;
   
   while( defined ($_ = $self->_readline )) {       
       next if( /^\s+$/); # skip empty lines
next if( /CPU time:/); next if( /^>\s*$/); if( /^([T]?BLAST[NPX])\s*(.+)$/i || /^(PSITBLASTN)\s+(.+)$/i || /^(RPS-BLAST)\s*(.+)$/i || /^(MEGABLAST)\s*(.+)$/i ) { if( $seentop ) { $self->_pushback($_); $self->in_element('hsp') && $self->end_element({ 'Name' => 'Hsp'}); $self->in_element('hit') && $self->end_element({ 'Name' => 'Hit'}); $self->end_element({ 'Name' => 'BlastOutput'}); return $self->end_document(); } $self->start_element({ 'Name' => 'BlastOutput' } ); $self->{'_result_count'}++; $seentop = 1; $reporttype = $1; $reportline = $_; # to fix the fact that RPS-BLAST output is wrong
$self->element({ 'Name' => 'BlastOutput_program', 'Data' => $reporttype}); $self->element({ 'Name' => 'BlastOutput_version', 'Data' => $2}); } elsif ( /^Query=\s*(.+)$/ ) { my $q = $1; my $size = 0; if( defined $seenquery ) { $self->_pushback($reportline); $self->_pushback($_); $self->in_element('hsp') && $self->end_element({'Name'=> 'Hsp'}); $self->in_element('hit') && $self->end_element({'Name'=> 'Hit'}); $self->end_element({'Name' => 'BlastOutput'}); return $self->end_document(); } else { if( ! defined $reporttype ) { $self->start_element({'Name' => 'BlastOutput'}); $seentop = 1; $self->{'_result_count'}++; } } $seenquery = $q; $_ = $self->_readline; while( defined ($_) ) { if( /^Database:/ ) { $self->_pushback($_); last; } chomp; if( /\((\-?[\d,]+)\s+letters.*\)/ ) { $size = $1; $size =~ s/,//g; last; } else { $q .= " $_"; $q =~ s/ +/ /g; $q =~ s/^ | $//g; } $_ = $self->_readline; } chomp($q); my ($nm,$desc) = split(/\s+/,$q,2); $self->element({ 'Name' => 'BlastOutput_query-def', 'Data' => $nm}); $self->element({ 'Name' => 'BlastOutput_query-len', 'Data' => $size}); defined $desc && $desc =~ s/\s+$//; $self->element({ 'Name' => 'BlastOutput_querydesc', 'Data' => $desc}); if( my @pieces = split(/\|/,$nm) ) { my $acc = pop @pieces; $acc = pop @pieces if( ! defined $acc || $acc =~ /^\s+$/); $self->element({ 'Name' => 'BlastOutput_query-acc', 'Data' => $acc}); } } elsif( /Sequences producing significant alignments:/ ) { descline: while( defined ($_ = $self->_readline() )) { if( /^>/ ) { $self->_pushback($_); last descline; } elsif( /(\d+)\s+([\d\.\-eE]+)(\s+\d+)?\s*$/) { # the last match is for gapped BLAST output
# which will report the number of HSPs for the Hit
my ($score, $evalue) = ($1, $2); # Some data clean-up so e-value will appear numeric to perl
$evalue =~ s/^e/1e/i; push @hit_signifs, [ $evalue, $score ]; } } } elsif( /Sequences producing High-scoring Segment Pairs:/ ) { # skip the next line
$_ = $self->_readline(); while( defined ($_ = $self->_readline() ) && ! /^\s+$/ ) { my @line = split; pop @line; # throw away first number which is for 'N'col
push @hit_signifs, [ pop @line, pop @line]; } } elsif ( /^Database:\s*(.+)$/ ) { my $db = $1; while( defined($_ = $self->_readline) ) { if( /^\s+(\-?[\d\,]+)\s+sequences\;\s+(\-?[\d,]+)\s+total\s+letters/){ my ($s,$l) = ($1,$2); $s =~ s/,//g; $l =~ s/,//g; $self->element({'Name' => 'BlastOutput_db-len', 'Data' => $s}); $self->element({'Name' => 'BlastOutput_db-let', 'Data' => $l}); last; } else { chomp; $db .= $_; } } $self->element({'Name' => 'BlastOutput_db', 'Data' => $db}); } elsif( /^>(\S+)\s*(.*)?/ ) { chomp; $self->in_element('hsp') && $self->end_element({ 'Name' => 'Hsp'}); $self->in_element('hit') && $self->end_element({ 'Name' => 'Hit'}); $self->start_element({ 'Name' => 'Hit'}); my $id = $1; my $restofline = $2; $self->element({ 'Name' => 'Hit_id', 'Data' => $id}); my ($acc, $version); if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|lcl)\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $2; } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $3; } else { #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README
#Database Name Identifier Syntax
#============================ ========================
#GenBank gb|accession|locus
#EMBL Data Library emb|accession|locus
#DDBJ, DNA Database of Japan dbj|accession|locus
#NBRF PIR pir||entry
#Protein Research Foundation prf||name
#SWISS-PROT sp|accession|entry name
#Brookhaven Protein Data Bank pdb|entry|chain
#Patents pat|country|number
#GenInfo Backbone Id bbs|number
#General database identifier gnl|database|identifier
#NCBI Reference Sequence ref|accession|locus
#Local Sequence identifier lcl|identifier
$acc=$id; } $self->element({ 'Name' => 'Hit_accession', 'Data' => $acc}); my $v = shift @hit_signifs; if( defined $v ) { $self->element({'Name' => 'Hit_signif', 'Data' => $v->[0]}); $self->element({'Name' => 'Hit_score', 'Data' => $v->[1]}); } while(defined($_ = $self->_readline()) ) { next if( /^\s+$/ ); chomp; if( /Length\s*=\s*([\d,]+)/ ) { my $l = $1; $l =~ s/\,//g; $self->element({ 'Name' => 'Hit_len', 'Data' => $l }); last; } else { $restofline .= $_; } } $restofline =~ s/\s+/ /g; $self->element({ 'Name' => 'Hit_def', 'Data' => $restofline}); } elsif( /\s+(Plus|Minus) Strand HSPs:/i ) { next; } elsif( ($self->in_element('hit') || $self->in_element('hsp')) && # wublast
m/Score\s*=\s*(\S+)\s* # Bit score
\(([\d\.]+)\s*bits\), # Raw score
\s*Expect\s*=\s*([^,\s]+), # E-value
\s*(?:Sum)?\s* # SUM
P(?:\(\d+\))?\s*=\s*([^,\s]+) # P-value
/ox
) {
my (
$score, $bits,$evalue,$pvalue) = ($1,$2,$3,$4);
$evalue =~ s/^e/1e/i; $pvalue =~ s/^e/1e/i; $self->in_element('hsp') && $self->end_element({'Name' => 'Hsp'}); $self->start_element({'Name' => 'Hsp'}); $self->element( { 'Name' => 'Hsp_score', 'Data' => $score}); $self->element( { 'Name' => 'Hsp_bit-score', 'Data' => $bits}); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $evalue}); $self->element( {'Name' => 'Hsp_pvalue', 'Data' => $pvalue}); } elsif( ($self->in_element('hit') || $self->in_element('hsp')) && # ncbi blast
m/Score\s*=\s*(\S+)\s*bits\s* # Bit score
(?:\((\d+)\))?, # Missing for BLAT pseudo-BLAST fmt
\s*Expect(?:\(\d+\))?\s*=\s*(\S+) # E-value
/ox) {
my (
$bits,$score,$evalue) = ($1,$2,$3);
$evalue =~ s/^e/1e/i; $self->in_element('hsp') && $self->end_element({ 'Name' => 'Hsp'}); $self->start_element({'Name' => 'Hsp'}); $self->element( { 'Name' => 'Hsp_score', 'Data' => $score}); $self->element( { 'Name' => 'Hsp_bit-score', 'Data' => $bits}); $self->element( { 'Name' => 'Hsp_evalue', 'Data' => $evalue}); } elsif( $self->in_element('hsp') && m/Identities\s*=\s*(\d+)\s*\/\s*(\d+)\s*[\d\%\(\)]+\s*
(?:,\s*Positives\s*=\s*(\d+)\/(\d+)\s*[\d\%\(\)]+\s*)? # pos only valid for Protein alignments
(?:\,\s*Gaps\s*=\s*(\d+)\/(\d+))? # Gaps
/oxi
) {
$self->element( { 'Name' => 'Hsp_identity',
'Data' => $1});
$self->element( {'Name' => 'Hsp_align-len', 'Data' => $2}); if( defined $3 ) { $self->element( { 'Name' => 'Hsp_positive', 'Data' => $3}); } else { $self->element( { 'Name' => 'Hsp_positive', 'Data' => $1}); } if( defined $6 ) { $self->element( { 'Name' => 'Hsp_gaps', 'Data' => $5}); } $self->{'_Query'} = { 'begin' => 0, 'end' => 0}; $self->{'_Sbjct'} = { 'begin' => 0, 'end' => 0}; if( /(Frame\s*=\s*.+)$/ ) { # handle wu-blast Frame listing on same line
$self->_pushback($1); } } elsif( $self->in_element('hsp') && /Strand\s*=\s*(Plus|Minus)\s*\/\s*(Plus|Minus)/i ) { # consume this event ( we infer strand from start/end)
next; } elsif( $self->in_element('hsp') && /Frame\s*=\s*([\+\-][1-3])\s*(\/\s*([\+\-][1-3]))?/ ){ my ($one,$two)= ($1,$2); my ($queryframe,$hitframe); if( $reporttype eq 'TBLASTX' ) { ($queryframe,$hitframe) = ($one,$two); $hitframe =~ s/\/\s*//g; } elsif( $reporttype =~ /^(PSI)?TBLASTN/oi ) { ($hitframe,$queryframe) = ($one,0); } elsif( $reporttype eq 'BLASTX' ) { ($queryframe,$hitframe) = ($one,0); } $self->element({'Name' => 'Hsp_query-frame', 'Data' => $queryframe}); $self->element({'Name' => 'Hsp_hit-frame', 'Data' => $hitframe}); } elsif( /^Parameters:/ || /^\s+Database:\s+?/ || /^\s+Subset/ || /^\s+Subset/ || /^\s*Lambda/ || /^\s*Histogram/ || ( $self->in_element('hsp') && /WARNING|NOTE/ ) ) { $self->in_element('hsp') && $self->end_element({'Name' => 'Hsp'}); $self->in_element('hit') && $self->end_element({'Name' => 'Hit'}); next if /^\s+Subset/; my $blast = ( /^(\s+Database\:)|(\s*Lambda)/ ) ? 'ncbi' : 'wublast'; if( /^\s*Histogram/ ) { $blast = 'btk'; } my $last = ''; # default is that gaps are allowed
$self->element({'Name' => 'Parameters_allowgaps', 'Data' => 'yes'}); while( defined ($_ = $self->_readline ) ) { if( /^(PSI)?([T]?BLAST[NPX])\s*(.+)$/i || /^(RPS-BLAST)\s*(.+)$/i || /^(MEGABLAST)\s*(.+)$/i ) { $self->_pushback($_); # let's handle this in the loop
last; } elsif( /^Query=/ ) { $self->_pushback($reportline); $self->_pushback($_); # -- Superfluous I think
$self->in_element('hsp') && $self->end_element({'Name' => 'Hsp'}); $self->in_element('hit') && $self->end_element({'Name' => 'Hit'}); # --
$self->end_element({ 'Name' => 'BlastOutput'}); return $self->end_document(); } # here is where difference between wublast and ncbiblast
# is better handled by different logic
if( /Number of Sequences:\s+([\d\,]+)/i || /of sequences in database:\s+([\d,]+)/i) { my $c = $1; $c =~ s/\,//g; $self->element({'Name' => 'Statistics_db-len', 'Data' => $c}); } elsif ( /letters in database:\s+(\-?[\d,]+)/i) { my $s = $1; $s =~ s/,//g; $self->element({'Name' => 'Statistics_db-let', 'Data' => $s}); } elsif( $blast eq 'btk' ) { next; } elsif( $blast eq 'wublast' ) { if( /E=(\S+)/ ) { $self->element({'Name' => 'Parameters_expect', 'Data' => $1}); } elsif( /nogaps/ ) { $self->element({'Name' => 'Parameters_allowgaps', 'Data' => 'no'}); } elsif( $last =~ /(Frame|Strand)\s+MatID\s+Matrix name/i ){ s/^\s+//; #throw away first two slots
my @vals = split; splice(@vals, 0,2); my ($matrix,$lambda,$kappa,$entropy) = @vals; $self->element({'Name' => 'Parameters_matrix', 'Data' => $matrix}); $self->element({'Name' => 'Statistics_lambda', 'Data' => $lambda}); $self->element({'Name' => 'Statistics_kappa', 'Data' => $kappa}); $self->element({'Name' => 'Statistics_entropy', 'Data' => $entropy}); } elsif( m/^\s+Q=(\d+),R=(\d+)\s+/ox ) {
$self->element({'Name' => 'Parameters_gap-open',
'Data' =>
$1});
$self->element({'Name' => 'Parameters_gap-extend', 'Data' => $2}); } elsif( /(\S+\s+\S+)\s+DFA:\s+(\S+)\s+\((.+)\)/ ) { if( $1 eq 'states in') { $self->element({'Name' => 'Statistics_DFA_states', 'Data' => "$2 $3"}); } elsif( $1 eq 'size of') { $self->element({'Name' => 'Statistics_DFA_size', 'Data' => "$2 $3"}); } } elsif( /^\s+Time to generate neighborhood:\s+(\S+\s+\S+\s+\S+)/ ) { $self->element({'Name' => 'Statistics_neighbortime', 'Data' => $1}); } elsif( /processors\s+used:\s+(\d+)/ ) { $self->element({'Name' => 'Statistics_noprocessors', 'Data' => $1}); } elsif( m/^\s+(\S+)\s+cpu\s+time:\s+(\S+\s+\S+\s+\S+)\s+
Elapsed:\s+(\S+)/ox ) {
my
$cputype = lc($1);
$self->element({'Name' => "Statistics_$cputype\_cputime", 'Data' => $2}); $self->element({'Name' => "Statistics_$cputype\_actualtime", 'Data' => $3}); } elsif( /^\s+Start:/ ) { my ($junk,$start,$stime,$end,$etime) = split(/\s+(Start|End)\:\s+/,$_); chomp($stime); $self->element({'Name' => 'Statistics_starttime', 'Data' => $stime}); chomp($etime); $self->element({'Name' => 'Statistics_endtime', 'Data' => $etime}); } elsif( !/^\s+$/ ) { $self->debug( "unmatched stat $_"); } } elsif ( $blast eq 'ncbi' ) { if( m/^Matrix:\s+(\S+)/oxi ) {
$self->element({'Name' => 'Parameters_matrix',
'Data' =>
$1});
} elsif( /Lambda/ ) { $_ = $self->_readline; s/^\s+//; my ($lambda, $kappa, $entropy) = split; $self->element({'Name' => 'Statistics_lambda', 'Data' => $lambda}); $self->element({'Name' => 'Statistics_kappa', 'Data' => $kappa}); $self->element({'Name' => 'Statistics_entropy', 'Data' => $entropy}); } elsif( m/effective\s+search\s+space\s+used:\s+(\d+)/ox ) {
$self->element({'Name' => 'Statistics_eff-spaceused',
'Data' =>
$1});
} elsif( m/effective\s+search\s+space:\s+(\d+)/ox ) {
$self->element({'Name' => 'Statistics_eff-space',
'Data' =>
$1});
} elsif( m/Gap\s+Penalties:\s+Existence:\s+(\d+)\,
\s+Extension:\s+(\d+)/ox) {
$self->element({'Name' => 'Parameters_gap-open',
'Data' =>
$1});
$self->element({'Name' => 'Parameters_gap-extend', 'Data' => $2}); } elsif( /effective\s+HSP\s+length:\s+(\d+)/ ) { $self->element({'Name' => 'Statistics_hsp-len', 'Data' => $1}); } elsif( /effective\s+length\s+of\s+query:\s+([\d\,]+)/ ) { my $c = $1; $c =~ s/\,//g; $self->element({'Name' => 'Statistics_query-len', 'Data' => $c}); } elsif( m/effective\s+length\s+of\s+database:\s+
([\d\,]+)/ox){
my
$c = $1;
$c =~ s/\,//g; $self->element({'Name' => 'Statistics_eff-dblen', 'Data' => $c}); } elsif( m/^(T|A|X1|X2|S1|S2):\s+(.+)/ox ) {
my
$v = $2;
chomp($v); $self->element({'Name' => "Statistics_$1", 'Data' => $v}); } elsif( m/frameshift\s+window\,\s+decay\s+const:\s+
(\d+)\,\s+([\.\d]+)/ox ) {
$self->element({'Name'=> 'Statistics_framewindow',
'Data' =>
$1});
$self->element({'Name'=> 'Statistics_decay', 'Data' => $2}); } elsif( m/^Number\s+of\s+Hits\s+to\s+DB:\s+(\S+)/ox ) {
$self->element({'Name' => 'Statistics_hit_to_db',
'Data' =>
$1});
} elsif( m/^Number\s+of\s+extensions:\s+(\S+)/ox ) {
$self->element({'Name' => 'Statistics_num_extensions',
'Data' =>
$1});
} elsif( m/^Number\s+of\s+successful\s+extensions:\s+
(\S+)/ox ) {
$self->element({'Name' => 'Statistics_num_suc_extensions',
'Data' =>
$1});
} elsif( m/^Number\s+of\s+sequences\s+better\s+than\s+
(\S+):\s+(\d+)/ox ) {
$self->element({'Name' => 'Parameters_expect',
'Data' =>
$1});
$self->element({'Name' => 'Statistics_seqs_better_than_cutoff', 'Data' => $2}); } elsif( /^\s+Posted\s+date:\s+(.+)/ ) { my $d = $1; chomp($d); $self->element({'Name' => 'Statistics_posted_date', 'Data' => $d}); } elsif( ! /^\s+$/ ) { $self->debug( "unmatched stat $_"); } } $last = $_; } } elsif( $self->in_element('hsp') ) { # let's read 3 lines at a time;
my %data = ( 'Query' => '', 'Mid' => '', 'Hit' => '' ); my ($l,$len); for( my $i = 0; defined($_) && $i < 3; $i++ ){ chomp; if( ($i == 0 && /^\s+$/) || ($l = /^\s*Lambda/i) ) { $self->_pushback($_) if defined $_; # this fixes bug #1443
$self->end_element({'Name' => 'Hsp'}); $self->end_element({'Name' => 'Hit'}) if $l; last; } if( /^((Query|Sbjct):\s+(\d+)\s*)(\S+)\s+(\d+)/ ) { $data{$2} = $4; $len = length($1); $self->{"\_$2"}->{'begin'} = $3 unless $self->{"_$2"}->{'begin'}; $self->{"\_$2"}->{'end'} = $5; } else { $self->throw("no data for midline $_") unless (defined $_ && defined $len); $data{'Mid'} = substr($_,$len); } $_ = $self->_readline(); } $self->characters({'Name' => 'Hsp_qseq', 'Data' => $data{'Query'} }); $self->characters({'Name' => 'Hsp_hseq', 'Data' => $data{'Sbjct'}}); $self->characters({'Name' => 'Hsp_midline', 'Data' => $data{'Mid'} }); } else { $self->debug( "unrecognized line $_"); } } if( $seentop ) { # double back check that hits and hsps are closed
# this in response to bug #1443 (may be uncessary due to fix
# above, but making double sure)
$self->in_element('hsp') && $self->end_element({'Name' => 'Hsp'}); $self->in_element('hit') && $self->end_element({'Name' => 'Hit'}); $self->end_element({'Name' => 'BlastOutput'}); } # $self->end_element({'Name' => 'BlastOutput'}) unless ! $seentop;
return $self->end_document();
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_elements'} = [];
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($self,$data) = @_;
   # we currently don't care about attributes
my $nm = $data->{'Name'}; my $type = $MODEMAP{$nm}; if( $type ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; if( $type eq 'result') { $self->{'_values'} = {}; $self->{'_result'}= undef; } else { # cleanup some things
if( defined $self->{'_values'} ) { foreach my $k ( grep { /^\U$type\-/ } keys %{$self->{'_values'}} ) { delete $self->{'_values'}->{$k}; } } } }
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($self,$name) = @_;  
   return 0 if ( ! defined $name &&
		 ! defined  $self->{'_elements'} ||
		 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       if( $_ eq $name  ) {
	   return 1;
       } 
   }
   return 0;
}
write_resultdescriptionprevnextTop
sub write_result {
   my ($self, $blast, @args) = @_;

   if( not defined($self->writer) ) {
       $self->warn("Writer not defined. Using a $DEFAULT_BLAST_WRITER_CLASS");
       $self->writer( $DEFAULT_BLAST_WRITER_CLASS->new() );
   }
   $self->SUPER::write_result( $blast, @args );
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $obj = new Bio::SearchIO::blast();
Function: Builds a new Bio::SearchIO::blast object
Returns : Bio::SearchIO::blast
Args : -fh/-file => filehandle/filename to BLAST file
-format => 'blast'