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