Bio::Matrix::PSM::IO::mast(3)

NAME
Bio::Matrix::PSM::IO::mast - PSM mast parser implementation

SYNOPSIS
See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers

DESCRIPTION
Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM sequence matches, than to PSM themselves.

TO DO
Section III should be parsed too, otherwise no real sequence is available, so we supply 'NNNNN....' as a seq which is not right.

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
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 Title   : new
 Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'mast',
                                                 -file=>$file);
 Function: Associates a file with the appropriate parser
 Throws  : Throws if the file passed is in HTML format or if
           some criteria for the file
           format are not met.
 Example :
 Returns : psm object, associated with a file with matrix file
 Args    : hash
 return  : "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  : Throws if there ara format violations in the input file (checking is not
            very strict with all drivers).
 Example :
 Returns : Bio::Matrix::PSM::Psm object
 Args    : none