Raw content of Bio::SearchIO::fasta
<![CDATA[# $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;
]]>