|Bio::Matrix::PSM::IO::mast(3pm)||User Contributed Perl Documentation||Bio::Matrix::PSM::IO::mast(3pm)|
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.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
AUTHOR - Stefan Kirov¶
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'mast', -file=>$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);
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'); $psmio->write_psm($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 :