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

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    :