/usr/lib/perl5/TFBS/PatternGen/Gibbs.pm is in libtfbs-perl 0.6.0+dfsg-1.
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#
# Copyright Boris Lenhard
#
# You may distribute this module under the same terms as perl itself
#
# POD
=head1 NAME
TFBS::PatternGen::Gibbs - a pattern factory that uses Chip Lawrences Gibbs program
=head1 SYNOPSIS
my $patterngen =
TFBS::PatternGen::Gibbs->new(-seq_file=>'sequences.fa',
-binary => '/Programs/Gibbs-1.0/bin/Gibbs'
-nr_hits => 24,
-motif_length => [8, 9, 10],
-additional_params => '-x -r -e');
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
=head1 DESCRIPTION
TFBS::PatternGen::Gibbs builds position frequency matrices
using an advanced Gibbs sampling algorithm implemented in external
I<Gibbs> program by Chip Lawrence. The algorithm can produce
multiple patterns from a single set of sequences.
=cut
package TFBS::PatternGen::Gibbs;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from TFBS::PatternGen;
use TFBS::PatternGen;
use TFBS::PatternGen::Gibbs::Motif;
use File::Temp qw(:POSIX);
use Bio::Seq;
use Bio::SeqIO;
@ISA = qw(TFBS::PatternGen);
=head2 new
Title : new
Usage : my $db = TFBS::PatternGen::Gibbs->new(%args);
Function: the constructor for the TFBS::PatternGen::Gibbs object
Returns : a TFBS::PatternGen::Gibbs object
Args : This method takes named arguments;
you must specify one of the following three
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
Other arguments are:
-binary # a fully qualified path to Gibbs executable
# OPTIONAL: default 'Gibbs'
-nr_hits # a presumed number of pattern occurences in the
# sequence set: it can be a single integer, e.g.
# -nr_hits => 24 , or a reference to an array of
# integers, e.g -nr_hits => [12, 24, 36]
-motif_length # an expected length of motif in nucleotides:
# it can be a single integer, e.g.
# -motif_length => 8 , or a reference to an
# array ofintegers, e.g -motif_length => [8..12]
-additional_params # a string containing additional
# command-line switches for the
# Gibbs program
=cut
sub new {
my ($caller, %args) = @_;
my $self = bless {}, ref($caller) || $caller;
$self->{'motif_length_string'} =
($args{'-motif_length'}
? (ref($args{'-motif_length'})
? join(',', @{$args{'-motif_length'}})
: $args{'-motif_length'})
: 8 );
$self->{'nr_hits_string'} =
($args{'-nr_hits'}
? (ref($args{'-nr_hits'})
? join(',', @{$args{'-nr_hits'}})
: $args{'-nr_hits'})
: "" );
$self->{'additional_params'} =
($args{'-additional_params'}
? (ref($args{'-additional_params'})
? join(' ', @{$args{'-additional_params'}})
: $args{'-additional_params'})
: "" );
$self->{'binary'} = $args{'-binary'} || 'Gibbs';
$self->{'motifs'} = [];
$self->_create_seq_set(%args) or die ('Error creating sequence set');
#print $self->{'seq_set'}->[0]->seq;
#$self->_seq_props;
$self->_run_Gibbs() or $self->throw("Error running Gibbs.");
return $self;
}
sub _run_Gibbs {
my $self = shift;
my $tmp_file = tmpnam();
my $outstream = Bio::SeqIO->new(-file=>">$tmp_file", -format=>"fasta");
foreach my $seqobj (@{ $self->{'seq_set'} } ) {
$outstream->write_seq($seqobj);
}
$outstream->close();
my $command_line =
$self->{'binary'}." ".
" -PBernoulli ".
$tmp_file." ".
$self->{'motif_length_string'}." ".
$self->{'nr_hits_string'}." ".
$self->{'additional_params'}." -n";
my $resultstring = `$command_line`;
$self->_parse_Gibbs_output($resultstring);
#print STDERR "$command_line\n";
#print STDERR $resultstring;
unlink $tmp_file;
return 1
}
=head2 pattern
=head2 all_patterns
=head2 patternSet
The three methods listed above are used for the retrieval of patterns,
and are common to all TFBS::PatternGen::* classes. Please
see L<TFBS::PatternGen> for details.
=cut
sub _parse_Gibbs_output {
my ($self, $resultstring) = @_;
#print $resultstring;
#print"===========END_RESULTSTRING===============================\n";
$resultstring =~ s/.*=== MAP MAXIMIZATION RESULTS ===//s;
my @raw_motifs = split /\-+\n\s+MOTIF \w\n/s, $resultstring;
shift @raw_motifs; # discard the first one
foreach my $raw_motif (@raw_motifs) {
#print $raw_motif;
my $motif =$self->_parse_raw_motif($raw_motif) || next;
push @{ $self->{'motifs'} }, $motif;
}
return 1;
}
sub _site_props{
my ($self,$raw_motif)=@_;
my @sites;
# print $raw_motif;
$raw_motif=~s/.*Num Motifs:\s+\d+\n//s;
# print $raw_motif;
#print "#####################################################\n";
$raw_motif=~s/\n\s+\*+.*//s;
#print $raw_motif,"\n";
my @site_lines=(split("\n", $raw_motif));
foreach my $site(@site_lines){
my $start_seq;
my $end_seq;
my ($seq_nr,$pattern_nr,$start,$seq,$end,$score,$strand,$desc)=$site=~/\s+(\d+),\s+(\d+)\s+(\d+)\s+([\w,\s]+)\s+(\d+)\s+(\d\.\d+)\s+([F,R])(.*)/;
# print $seq_nr,$pattern_nr,$start,$seq;
if ($strand eq "F"){
$strand=1;
$start_seq=$start;
$end_seq=$end;
}
else{
$strand=-1;
$start_seq=$end;
$end_seq=$start;
}
#print $site;
my $site = Bio::SeqFeature::Generic->new ( -start => $start_seq,
-end => $end_seq,
-strand => $strand,
-source => 'Gibbs sampler',
-score => $score,
);
$site->attach_seq ($self->{'seq_set'}->[$seq_nr-1]);
push (@sites,$site);
}
foreach my $site(@sites){
#print $site->start."\n";
}
return \@sites;
}
sub _parse_raw_motif {
# a utility function
my ($self,$raw_motif) = @_;
# print $raw_motif;
my ($raw_matrix, $raw_bp, $length, $nr_hits, $MAP_score) =
$raw_motif =~ /Motif model \(residue frequency x 100\)\n(.+)Motif probability model\n.+Background probability model\n\s+(.+?)\n.+\D(\d+) columns\nNum Motifs\: (\d+).+Difference of Logs of Maps = ([\-\.\d]+)\n/s;
#print $raw_matrix;
return undef unless $raw_matrix;
my $sites = $self->_site_props($raw_motif);
# print STDERR
# join ":", ($raw_matrix, $raw_bp, $length, $nr_hits); print "\n";
my $matrix = _parse_raw_matrix($raw_matrix);
#print $matrix;
return
TFBS::PatternGen::Gibbs::Motif->new
#This object does not contain a new method. Instead the new method is than searched in the first ISA package. Remember that the object is still a TFBS::PatternGen::Gibbs::Motif.
#The only ISA in the package is TFBS::PatternGen::Motif.pm. This package indeed contains the new method
(-length => $length."",
-bg_probabilities => [split /\s+/, $raw_bp],
-MAP_score => $MAP_score,
-tags => {MAP_score => $MAP_score},
-nr_hits => $nr_hits,
-sites=>$sites,
-matrix => $matrix );
}
sub _parse_raw_matrix {
# a utility function
my $raw_matrix = shift;
my @lines = split "\n", $raw_matrix;
my (@A, @C, @G, @T);
foreach my $line (@lines) {
my $value_string;
next unless ($value_string) = $line =~ /\s+\d+\s+\|\s+(.+)/;
$value_string =~ s/\./0/g;
my ($a, $t, $c, $g) = split /\s+/, $value_string;
push @A, $a;
push @C, $c;
push @G, $g;
push @T, $t;
}
# print STDERR join(" ",@A, "\n", @C, "\n", @G, "\n", @T, "\n");
return [\@A, \@C, \@G, \@T];
}
1;
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