Raw content of Bio::SearchIO::blast
<![CDATA[# $Id: blast.pm,v 1.42.2.14 2003/09/15 16:19:01 jason Exp $
#
# BioPerl module for Bio::SearchIO::blast
#
# 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::blast - Event generator for event based parsing of blast reports
=head1 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 ) {
# ...
}
}
}
=head1 DESCRIPTION
This object encapsulated the necessary methods for generating events
suitable for building Bio::Search objects from a BLAST report file.
Read the L<Bio::SearchIO> for more information about how to use this.
=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::blast;
use strict;
use vars qw(@ISA %MAPPING %MODEMAP $DEFAULT_BLAST_WRITER_CLASS);
use Bio::SearchIO;
@ISA = qw(Bio::SearchIO );
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';
}
=head2 new
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'
=cut
=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 $seentop = 0;
my ($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();
}
=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'};
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};
}
}
}
}
}
=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 $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;
}
=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'} && $data->{'Data'} !~ /^\s+$/ );
if( $self->in_element('hsp') &&
$data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
$self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
}
$self->{'_last_data'} = $data->{'Data'};
}
=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 ) {
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)
}
=head2 start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
=cut
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'}= undef;
$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 $self->{'_result'};
}
sub write_result {
my ($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 );
}
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
sub report_count { shift->result_count }
1;
]]>