/usr/lib/perl5/TFBS/PatternGen/Elph.pm is in libtfbs-perl 0.5.svn.20100421-1build1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 | # TFBS module for TFBS::PatternGen::Elph
#
# Copyright Wynand Alkema
#
# You may distribute this module under the same terms as perl itself
#
# POD
=head1 NAME
TFBS::PatternGen::Elph - a pattern factory that uses the Elph program
=head1 SYNOPSIS
my $patterngen =
TFBS::PatternGen::Elph->new(-seq_file=>'sequences.fa',
-binary => '/Elph/elph'
-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::Elph;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from TFBS::PatternGen;
use TFBS::PatternGen;
use TFBS::PatternGen::Elph::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 );
$self->{'additional_params'} =
($args{'-additional_params'}
? (ref($args{'-additional_params'})
? join(' ', @{$args{'-additional_params'}})
: $args{'-additional_params'})
: "" );
$self->{'binary'} = $args{'-binary'} || 'elph';
$self->{'motifs'} = [];
$self->_create_seq_set(%args) or die ('Error creating sequence set');
$self->_run_elph() or $self->throw("Error running elph.");
return $self;
}
sub _run_elph {
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();
$self->{'additional_params'}=~s/-b//;
#This removes a -b switch. This enables long output containgin info about the sites
my $command_line =
$self->{'binary'}." ".
$tmp_file." ".
"LEN=".$self->{'motif_length_string'}." ".
$self->{'additional_params'}." 2>/dev/null";
my $resultstring = `$command_line`;
$self->_parse_elph_output($resultstring,$command_line);
#print STDERR "$command_line\n";
#print STDERR $resultstring;
# unlink $tmp_file;
return 1
}
=head2 pattern
=head2 all_patterns
=head2 patternSet
The three methods listed above are used for the retrieval of patterns,
and are common to all TFBS::PatternGen::* classes. Please
see L<TFBS::PatternGen> for details.
=cut
sub _parse_elph_output {
my ($self, $resultstring,$command_line) = @_;
#print $resultstring;
if ($resultstring=~/^error/){
$self->throw ("Error running elp command:\n $command_line");
return;
}
#Motif after optimizing
#MAP for motif: 46.735 InfoPar=0.098
#
#Motif found:
#
#Background probability model:
# a c g t
# 0.30 0.20 0.19 0.31
#
#Background counts:
#a: 1456
#c: 948
#g: 909
#t: 1487
#
#
#Motif probability model:
#Pos: 1 2 3 4 5 6
#a 1.00 0.00 1.00 0.83 0.00 0.00
#c 0.00 0.00 0.00 0.00 0.00 0.17
#g 0.00 1.00 0.00 0.17 1.00 0.83
#t 0.00 0.00 0.00 0.00 0.00 0.00
#------------------------------------------
#Info 1.73 2.42 1.73 1.19 2.42 1.75
#
#Motif counts:
#a: 6 0 6 5 0 0
#c: 0 0 0 0 0 1
#g: 0 6 0 1 6 5
#t: 0 0 0 0 0 0
#
#
(my $MAP)=$resultstring=~/MAP for motif: (.*) InfoPar=/;
($resultstring)=~s/.*Motif counts:\n//s;
#print STDERR $resultstring;
my @array=split "\n",$resultstring;
my @matrix;
#print $array[0],"\n";
foreach (0..3){
my (@line)=split(/\s+/,$array[$_]);
#print "@line\n";
shift @line;
push @matrix,\@line;
# print "@line\n";
}
# print @matrix;
#print $resultstring;
my $sites=$self->_site_props($resultstring);
my $motif =TFBS::PatternGen::Elph::Motif->new
(
-tags => {score=>$MAP},#The score in this case is the E-value given in the output
-sites=>$sites,
-matrix => \@matrix
);
# Seq.no Pos ***** Motif ***** Prob D Seq.Id
# 1 354 ggatt AGAAGC cgccg 0.1389 -1 GAL1
# 2 636 caaag AGAAGG ttttt 0.6942 -1 GAL10
# 3 456 aaggc AGAAGG cagta 0.6942 -1 GAL2
# 4 444 aaagt AGAGGG ggtaa 0.1388 -1 GAL7
# 5 324 tagag AGAAGG agcaa 0.6942 -1 GAL80
# 6 165 gttac AGAAGG gccgc 0.6942 -1 GCY1
#$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,$resultstring)=@_;
my @sites;
# print $resultstring;
#($resultstring)=~s/.*Motif counts:\n//s;
my @array=split(/Seq\.no/,$resultstring);
#print $array[1];
my @sites_array=split "\n", $array[1];
foreach my $line(@sites_array){
# print $line;
next if $line=~/Pos/;
last if $line eq'';
my @site=split(/\s+/,$line);
# print $site[1],"\n";
my $nr=0;
$nr = 1 if $site[2]==1;
#A special case when the site startsat the first base.
#Then no preceding quence is given and the site array =shorter by 1
my $motif_seq=$site[4-$nr];
# print $motif_seq,"\n";
my $site = Bio::SeqFeature::Generic->new ( -start => $site[2],
-end => $site[2]+(length$motif_seq)-1,
-strand => 1,
#Always 1 with elph
-source => 'Elph',
-score => $site[-3],
);
foreach my $seq(@{$self->{'seq_set'}}){
if ($seq->id eq $site[-1]){#last element of the array
$site->attach_seq ($seq);
}
}
push (@sites,$site);
}
return \@sites;
}
1;
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