Provided by: libbio-perl-perl_1.7.2-2_all bug


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


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


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


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


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AUTHOR - Stefan Kirov



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

        Title   : new
        Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'mast',
        Function: Associates a file with the appropriate parser
        Throws  : Throws if the file passed is in HTML format or if
                  some criteria for the file
                  format are not met.
        Example :
        Returns : psm object, associated with a file with matrix file
        Args    : hash
        return  : "Bio::Matrix::PSM::$format"->new(@args);

        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

        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');
                   #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 :