Bio::Matrix::PSM::IO::transfac.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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    :