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


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


       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


       Parser for meme.


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AUTHOR - Stefan Kirov



        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);

        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 :

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

        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