Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Matrix::PSM::IO::transfac - PSM transfac parser


       See Bio::Matrix::PSM::IO for documentation




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AUTHOR - Stefan Kirov



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

        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

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

        Title   : _make_matrix
        Usage   :
        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    :