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

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 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