Bio::Matrix::PSM::transfac - PSM transfac parser See Bio::Matrix::PSM::IO for documentation #

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new
Title : new Usage : my $psmIO = new Bio::Matrix::PSM::IO(-format=>'transfac', -file=>$file); Function: Associates a file with the appropriate parser Throws : Example : Args : Returns : "Bio::Matrix::PSM::$format"->new(@args);

next_psm
Title : next_psm Usage : my $psm=$psmIO->next_psm(); Function: Reads the next PSM from the input file, associated with this object Throws : Upon finding a line, defining the matrix, where one or more positions are not defined, see _make_matrix Returns : Bio::Matrix::PSM::Psm object Args : none

_parseMatrix
Title : _parseMatrix Usage : Function: Parses a line Throws : Example : Internal stuff Returns : array (frequencies for A,C,G,T in this order). Args : string

_make_matrix
Title : _make_matrix Usage : Function: Throws : If a position is undefined, for example if you have line like this in the file you are parsing: 08 4,7,,9 Example : Internal stuff Returns : Args :