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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    :