Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

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

DESCRIPTION

       #

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Stefan Kirov

       Email skirov@utk.edu

APPENDIX

   new
        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);

   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    :