Bio::Matrix::PSM::IO::transfac - PSM transfac parser
See Bio::Matrix::PSM::IO for documentation
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Title : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'transfac',
-file=>$file);
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 :
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 :