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

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://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

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

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

   write_psm
        Title   : write_psm
        Usage   : #Get SiteMatrix object somehow (see Bio::Matrix::PSM::SiteMatrix)
                   my $matrix=$psmin->next_matrix;
                   #Create the stream
                   my $psmio=new(-file=>">psms.mast",-format=>'mast');
                   $psmio->write_psm($matrix);
                   #Will warn if only PFM data is contained in $matrix, recalculate the PWM
                   #based on normal distribution (A=>0.25, C=>0.25, etc)
        Function: writes pwm in mast format
        Throws  :
        Example :
        Args    : SiteMatrix object
        Returns :