Raw content of Bio::Tools::BPlite::Iteration
<![CDATA[# $Id: Iteration.pm,v 1.15 2002/06/19 00:27:49 jason Exp $
# Bioperl module Bio::Tools::BPlite::Iteration
# based closely on the Bio::Tools::BPlite modules
# Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf),
# Lorenz Pollak (lorenz@ist.org, bioperl port)
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# _history
# October 20, 2000
# POD documentation - main docs before the code
#
# Added to get a simple_align object for a psiblast run with the -m 6 flag /AE
#
=head1 NAME
Bio::Tools::BPlite::Iteration - object for parsing single iteration
of a PSIBLAST report
=head1 SYNOPSIS
use Bio::Tools:: BPpsilite;
open FH, "t/psiblastreport.out";
$report = Bio::Tools::BPpsilite->new(-fh=>\*FH);
# determine number of iterations executed by psiblast
$total_iterations = $report->number_of_iterations;
$last_iteration = $report->round($total_iterations);
# Process only hits found in last iteration ...
$oldhitarray_ref = $last_iteration->oldhits;
HIT: while($sbjct = $last_iteration->nextSbjct) {
$id = $sbjct->name;
$is_old = grep /\Q$id\E/, @$oldhitarray_ref;
if ($is_old ){next HIT;}
# do something with new hit...
}
=head2 ALIGNMENTS
# This assumed that you have $db pointing to a database, $out to an output file
# $slxdir to a directory and $psiout
# note the alignments can only be obtained if the flag "-m 6" is run.
# It might also be necessary to use the flag -v to get all alignments
#
my @psiparams = ('database' => $db , 'output' => $out, 'j' => 3, 'm' => 6,
'h' => 1.e-3 , 'F' => 'T' , 'Q' => $psiout );
my $factory = Bio::Tools::Run::StandAloneBlast->new(@psiparams);
my $report = $factory->blastpgp($seq);
my $total_iterations = $report->number_of_iterations();
my $last_iteration = $report->round($total_iterations);
my $align=$last_iteration->Align;
my $slxfile=$slxdir.$id.".slx";
my $slx = Bio::AlignIO->new('-format' => 'selex','-file' => ">".$slxfile );
$slx->write_aln($align);
=head1 DESCRIPTION
See the documentation for BPpsilite.pm for a description of the
Iteration.pm module.
=head1 AUTHORS - Peter Schattner
Email: schattner@alum.mit.edu
=head1 CONTRIBUTORS
Jason Stajich, jason@cgt.mc.duke.edu
=head1 ACKNOWLEDGEMENTS
Based on work of:
Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf),
Lorenz Pollak (lorenz@ist.org, bioperl port)
=head1 COPYRIGHT
BPlite.pm is copyright (C) 1999 by Ian Korf.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=cut
package Bio::Tools::BPlite::Iteration;
use strict;
use vars qw(@ISA);
use Bio::Root::Root; # root object to inherit from
use Bio::Tools::BPlite; #
use Bio::Tools::BPlite::Sbjct;
@ISA = qw(Bio::Root::Root);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
($self->{'PARENT'},$self->{'ROUND'}) =
$self->_rearrange([qw(PARENT
ROUND
)],@args);
$self->{'QUERY'} = $self->{'PARENT'}->{'QUERY'};
$self->{'LENGTH'} = $self->{'PARENT'}->{'LENGTH'};
if($self->_parseHeader) {$self->{'REPORT_DONE'} = 0} # there are alignments
else {$self->{'REPORT_DONE'} = 1} # empty report
return $self; # success - we hope!
}
=head2 query
Title : query
Usage : $query = $obj->query();
Function : returns the query object
Example :
Returns : query object
Args :
=cut
sub query {shift->{'QUERY'}}
=head2 qlength
Title : qlength
Usage : $len = $obj->qlength();
Returns : length of query
Args : none
=cut
sub qlength {shift->{'LENGTH'}}
=head2 newhits
Title : newhits
Usage : $newhits = $obj->newhits();
Returns : reference to an array listing all the hits
from the current iteration which were not identified
in the previous iteration
Args : none
=cut
sub newhits {shift->{'NEWHITS'}}
=head2 oldhits
Title : oldhits
Usage : $oldhits = $obj->oldhits();
Returns : reference to an array listing all the hits from
the current iteration which were identified and
above threshold in the previous iteration
Args : none
=cut
sub oldhits {shift->{'OLDHITS'}}
=head2 nextSbjct
Title : nextSbjct
Usage : $sbjct = $obj->nextSbjct();
Function : Method of iterating through all the Sbjct retrieved
from parsing the report
#Example : while ( my $sbjct = $obj->nextSbjct ) {}
Returns : next Sbjct object or undef if finished
Args :
=cut
sub nextSbjct {
my ($self) = @_;
$self->_fastForward or return undef;
#######################
# get all sbjct lines #
#######################
my $def = $self->_readline();
while(defined ($_ = $self->_readline) ) {
if ($_ !~ /\w/) {next}
elsif ($_ =~ /Strand HSP/) {next} # WU-BLAST non-data
elsif ($_ =~ /^\s{0,2}Score/) {$self->_pushback( $_); last}
elsif ($_ =~ /^(\d+) .* \d+$/) { # This is not correct at all
$self->_pushback($_); # 1: HSP does not work for -m 6 flag
$def = $1; # 2: length/name are incorrect
my $length = undef; # 3: Names are repeated many times.
my $sbjct = new Bio::Tools::BPlite::Sbjct('-name'=>$def,
'-length'=>$length,
'-parent'=>$self);
return $sbjct;
} # m-6
elsif ($_ =~ /^Parameters|^\s+Database:|^\s+Posted date:/) {
$self->_pushback( $_);
last;
} else {$def .= $_}
}
$def =~ s/\s+/ /g;
$def =~ s/\s+$//g;
$def =~ s/Length = ([\d,]+)$//g;
my $length = $1;
return 0 unless $def =~ /^>/;
$def =~ s/^>//;
####################
# the Sbjct object #
####################
my $sbjct = new Bio::Tools::BPlite::Sbjct('-name'=>$def,
'-length'=>$length,
'-parent'=>$self);
return $sbjct;
}
# This is added by /AE
=head2 Align
Title : Align
Usage : $SimpleAlign = $obj->Align();
Function : Method to obtain a simpleAlign object from psiblast
Example : $SimpleAlign = $obj->Align();
Returns : SimpleAlign object or undef if not found.
BUG : Only works if psiblast has been run with m 6 flag
Args :
=cut
sub Align {
use Bio::SimpleAlign;
my ($self) = @_;
$self->_fastForward or return undef;
my $lastline = $self->_readline();
return undef unless $lastline =~ /^QUERY/; # If psiblast not run correctly
my (%sequence,%first,%last,$num);
if ( $lastline =~ /^QUERY\s+(\d*)\s*([-\w]+)\s*(\d*)\s*$/){
my $name='QUERY';
my $start=$1;
my $seq=$2;
my $stop=$3;
$seq =~ s/-/\./g;
$start =~ s/ //g;
$stop =~ s/ //g;
$sequence{$name} .= $seq;
if ($first{$name} eq ''){$first{$name}=$start;}
if ($stop ne ''){$last{$name}=$stop;}
# print "FOUND:\t$seq\t$start\t$stop\n";
$num=0;
}
while(defined($_ = $self->_readline()) ){
chomp($_);
if ( $_ =~ /^QUERY\s+(\d+)\s*([\-A-Z]+)\s*(\+)\s*$/){
my $name='QUERY';
my $start=$1;
my $seq=$2;
my $stop=$3;
$seq =~ s/-/\./g;
$start =~ s/ //g;
$stop =~ s/ //g;
$sequence{$name} .= $seq;
if ($first{$name} eq '') { $first{$name} = $start;}
if ($stop ne '') { $last{$name}=$stop;}
$num=0;
} elsif ( $_ =~ /^(\d+)\s+(\d+)\s*([\-A-Z]+)\s*(\d+)\s*$/ ){
my $name=$1.".".$num;
my $start=$2;
my $seq=$3;
my $stop=$4;
$seq =~ s/-/\./g;
$start =~ s/ //g;
$stop =~ s/ //g;
$sequence{$name} .= $seq;
if ($first{$name} eq ''){$first{$name}=$start;}
if ($stop ne ''){$last{$name}=$stop;}
$num++;
}
}
my $align = new Bio::SimpleAlign();
my @keys=sort keys(%sequence);
foreach my $name (@keys){
my $nse = $name."/".$first{$name}."-".$last{$name};
my $seqobj = Bio::LocatableSeq->new( -seq => $sequence{$name},
-id => $name,
-name => $nse,
-start => $first{$name},
-end => $last{$name}
);
$align->add_seq($seqobj);
}
return $align;
}
# Start of internal subroutines.
sub _parseHeader {
my ($self) = @_;
my (@old_hits, @new_hits);
my $newhits_true = ($self->{'ROUND'} < 2) ? 1 : 0 ;
while(defined($_ = $self->_readline()) ) {
if ($_ =~ /(\w\w|.*|\w+.*)\s\s+(\d+)\s+([-\.e\d]+)$/) {
my $id = $1;
my $score= $2; #not used currently
my $evalue= $3; #not used currently
if ($newhits_true) { push ( @new_hits, $id);}
else { push (@old_hits, $id);}
}
elsif ($_ =~ /^Sequences not found previously/) {$newhits_true = 1 ;}
# This is changed for "-m 6" option /AE
elsif ($_ =~ /^>/ || $_ =~ /^QUERY/)
{
$self->_pushback($_);
$self->{'OLDHITS'} = \@old_hits;
$self->{'NEWHITS'} = \@new_hits;
return 1;
}
elsif ($_ =~ /^Parameters|^\s+Database:|^\s*Results from round\s+(d+)/) {
$self->_pushback($_);
return 0; # no sequences found in this iteration
}
}
return 0; # no sequences found in this iteration
}
sub _fastForward {
my ($self) = @_;
return 0 if $self->{'REPORT_DONE'}; # empty report
while(defined($_ = $self->_readline()) ) {
if( $_ =~ /^>/ ||
$_ =~ /^QUERY|^\d+ .* \d+$/ ) { # Changed to also handle "-m 6" /AE
$self->_pushback($_);
return 1;
}
# print "FASTFORWARD",$_,"\n";
if ($_ =~ /^>|^Parameters|^\s+Database:/) {
$self->_pushback($_);
return 1;
}
}
$self->warn("Possible error (2) while parsing BLAST report!");
}
=head2 _readline
Title : _readline
Usage : $obj->_readline
Function: Reads a line of input.
Note that this method implicitely uses the value of $/ that is
in effect when called.
Note also that the current implementation does not handle pushed
back input correctly unless the pushed back input ends with the
value of $/.
Example :
Returns :
=cut
sub _readline{
my ($self) = @_;
return $self->{'PARENT'}->_readline();
}
=head2 _pushback
Title : _pushback
Usage : $obj->_pushback($newvalue)
Function: puts a line previously read with _readline back into a buffer
Example :
Returns :
Args : newvalue
=cut
sub _pushback {
my ($self, $arg) = @_;
return $self->{'PARENT'}->_pushback($arg);
}
1;
__END__
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