TFBS::PatternGen
YMF
Summary
TFBS::PatternGen::MEME - a pattern factory that uses the MEME program
Package variables
No package variables defined.
Included modules
Bio::Seq
Bio::SeqIO
File::Temp(1) qw ( :POSIX )
File::Temp(2) qw / tempfile tempdir /
Inherit
Synopsis
my $patterngen =
TFBS::PatternGen::MEME->new(-seq_file=>'sequences.fa',
-binary => 'meme'
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
Description
TFBS::PatternGen::MEME builds position frequency matrices
using an external program MEME written by Bailey and Elkan.
For information and source code of MEME see
http://www.sdsc.edu/MEME
Methods
Methods description
Title : new Usage : my $patterngen = TFBS::PatternGen::YMF->new(%args); Function: the constructor for the TFBS::PatternGen::MEME object Returns : a TFBS::PatternGen::MEME object Args : This method takes named arguments; you must specify one of the following three -seq_list # a reference to an array of strings # and/or Bio::Seq objects # or -seq_stream # A Bio::SeqIO object # or -seq_file # the name of the fasta file containing # all the sequences Other arguments are: -binary # a fully qualified path to the 'meme' executable # OPTIONAL: default 'meme' -additional_params # a string containing additional # command-line switches for the # meme program |
Methods code
_parse_stats_output | description | prev | next | Top |
sub _parse_stats_output
{ my ($self,$resultstring,$command_line,$dumpfile,$temp_dir)=@_;
open DUMP,$dumpfile;
while(<DUMP>){
if ((/(^Error.*)/) or /(.*Aborting.*)/){
print "YMF Error message:\" $1\"\n";
unlink $dumpfile;
$self->throw ("Error running YMF using command:\n $command_line");
return;
}
}
unlink $dumpfile;
open RES,"$temp_dir/results";
my $skip=<RES>;
while (<RES>){
my ($word,$occ,$z_score,$expect,$var)=split;
my $motif =TFBS::PatternGen::YMF::Motif->new
(-word=>$word,
-tags => {z_score=>$z_score,
'occurences'=>$occ,
'expectation value'=>$expect,
'variance'=>$var}
);
push @{ $self->{'motifs'} }, $motif;
}
my $command="rm -r $temp_dir";
`$command`;
}
1; } |
sub _run_stats
{ my ($self)=shift;
my $tmp_file = tmpnam();
my $dumpfile = tmpnam();
my $outstream = Bio::SeqIO->new(-file=>">$tmp_file", -format=>"fasta");
foreach my $seqobj (@{ $self->{'seq_set'} } ) {
$outstream->write_seq($seqobj);
}
$outstream->close();
my $dir = tempdir();
my $command_line =
$self->{'abs_stats_path'}."/stats ".
$self->{'config_file'}." ".
$self->{'len_region'}." ".
$self->{'width'}." ".
$self->{'path_org'}." ".
"-sort ". $tmp_file
." >$dumpfile"
;
my $resultstring = `cd $dir;$command_line`;
$self->_parse_stats_output($resultstring,$command_line,$dumpfile,$dir);
unlink $tmp_file;
return 1
}
} |
sub new
{ my ($caller, %args) = @_;
my $self = bless {}, ref($caller) || $caller;
$self->{'width'}=$args{'-length_oligo'};
$self->{'path_org'}=$args{'-pathoforganismtables'};
$self->{'len_region'}=$args{'-length_region'};
$self->{'config_file'}=$args{'-config_file'}||$args{'-stats_path'}."/stats.config";
$self->{'abs_stats_path'} = $args{'-abs_stats_path'} ;
$self->_create_seq_set(%args) or die ('Error creating sequence set');
$self->_run_stats() or $self->throw("Error running stats.");
return $self; } |
General documentation
Please send bug reports and other comments to the author.
AUTHOR - Wynand Alkema | Top |
Wynand Alkema <Wynand.Alkema@cgb.ki.se>
The three methods listed above are used for the retrieval of patterns,
and are common to all TFBS::PatternGen::* classes. Please
see
TFBS::PatternGen for details.