/ 
bioperl-1.4
/ Bio::Matrix::PSM::IO::transfac

NAME

Bio::Matrix::PSM::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://bio.perl.org/MailList.html     - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR - Stefan Kirov

Email skirov@utk.edu

APPENDIX

new

 Title   : new
 Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'transfac', 
						 -file=>$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    :