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

NAME

       Bio::Matrix::PSM::IO::masta - motif fasta format parser

SYNOPSIS

       MASTA is a position frequency matrix format similar to fasta. It contains one ID row just
       like fasta and then the actual data, which is tab delimited:

         0.1   0.62    .017    0.11
         0.22  0.13    0.54    0.11

       Or A,C,G and T could be horizontally positioned (positioning is automatically detected).
       Please note masta will parse only DNA at the moment.

       It will also convert a set of aligned sequences: ACATGCAT ACAGGGAT ACAGGCAT ACCGGCAT

       to a PFM (SiteMatrix object). When writing if you supply SEQ it will write 10 random
       instances, which represent correctly the frequency and can be used as an input for weblogo
       creation purposes.

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

DESCRIPTION

       Parser for meme.

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

   new
        Title   : new
        Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=> 'masta',
                                                        -file  => $file,
                                                        -mtype => 'PWM');
        Function: Associates a file with the appropriate parser
        Throws  :
        Example :
        Args    : hash
        Returns : "Bio::Matrix::PSM::$format"->new(@args);

   write_psm
        Title   : write_psm
        Usage   :
        Function: writes a pfm/pwm/raw sequence in a simple masta format
        Throws  :
        Example :
        Args    : SiteMatrix object, type (optional string: PWM, SEQ or PFM)
        Returns :

   next_matrix
         Title   : next_matrix
         Usage   : my $matrix = $psmio->next_matrix;
         Function: Alias of next_psm function

   next_psm
        Title   : next_psm
        Usage   : my $matrix=$psmio->next_psm;
        Function: returns the next matrix in the stream
        Throws  : If there is you mix different types, for example weights and
                  frequencies occur in the same entry You can mix weights, but these
                  should be designated by different ID lines
        Example :
        Args    :
        Returns : Bio::Matrix::PSM::SiteMatrix