Provided by: libtfbs-perl_0.7.0+dfsg-1build1_amd64
TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory
my @sequences = qw( AAGCCT AGGCAT AAGCCT AAGCCT AGGCAT AGGCCT AGGCAT AGGTTT AGGCAT AGGCCT AGGCCT ); my $patterngen = TFBS::PatternGen::SimplePFM->new(-seq_list=>\@sequences); my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set of nucleotide sequences of equal length, The sequences can be passed either as strings, as Bio::Seq objects or as a fasta file. This pattern generator always creates only one pattern from a given set of sequences. new Title : new Usage : my $db = TFBS::PatternGen::SimplePFM->new(%args); Function: the constructor for the TFBS::PatternGen::SimplePFM object Returns : a TFBS::PatternGen::SimplePFM obkect Args : This method takes named arguments; you must specify one of the following -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 pattern all_patterns patternSet The three above methods are used fro the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see TFBS::PatternGen for details.