NAME

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

SYNOPSIS

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

DESCRIPTION

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

TO DO

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

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

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

new

            

              
              
Title   : new
Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'mast', 
                                                                       -file=>$file);
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);
            
          

next_psm

            

              
              
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
            
          

write_psm

            

              
              
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');
           $psmio->write_psm($matrix);
           #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 :