Bio::Tools::Run::Genemark - Wrapper for local execution of the GeneMark family of programs.
# GeneMark.hmm (prokaryotic) my $factory = Bio::Tools::Run::Genemark->new('-program' => 'gmhmmp', '-m' => 'model.icm'); # Pass the factory Bio::Seq objects # returns a Bio::Tools::Genemark object my $genemark = $factory->run($seq);
Wrapper module for the GeneMark family of programs. Should work with all flavors of GeneMark.hmm at least, although only the prokaryotic version has been tested.
General information about GeneMark is available at http://exon.gatech.edu/GeneMark/.
Contact information for licensing inquiries is available at: http://opal.biology.gatech.edu/GeneMark/contact.html
Note that GeneMark.hmm (prokaryotic at least) will only process the first sequence in a fasta file (if you run() more than one sequence at a time, only the first will be processed).
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.
email@example.com - 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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: gets/sets the program name Returns: string Args : string
Title : program_dir Usage : $factory->program_dir() Function: gets/sets the program dir Returns: string Args : string
Title : new Usage : $genemark->new(@params) Function: creates a new Genemark factory Returns: Bio::Tools::Run::Genemark Args :
Title : run Usage : $obj->run($seq_file) Function: Runs Genemark Returns : A Bio::Tools::Genemark object Args : An array of Bio::PrimarySeqI objects
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An instance of Bio::Tools::Genemark Args : file name, sequence identifier (optional)
Title : _write_seq_file Usage : obj->_write_seq_file($seq) or obj->_write_seq_file(@seq) Function: Internal(not to be used directly) Returns : Name of a temp file containing program output Args : One or more Bio::PrimarySeqI objects