Bio::Matrix::PSM::IO::mast - 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.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email skirov@utk.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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