NAME

Bio::Tools::Run::Genemark - Wrapper for local execution of the GeneMark family of programs.

SYNOPSIS

  # 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);

DESCRIPTION

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).

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:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark Johnson

 Email: johnsonm-at-gmail-dot-com

APPENDIX

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

program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: gets/sets the program name
 Returns:  string
 Args    : string

program_dir

 Title   : program_dir
 Usage   : $factory->program_dir()
 Function: gets/sets the program dir
 Returns:  string
 Args    : string

new

 Title   : new
 Usage   : $genemark->new(@params)
 Function: creates a new Genemark factory
 Returns:  Bio::Tools::Run::Genemark
 Args    :

run

 Title   :   run
 Usage   :   $obj->run($seq_file)
 Function:   Runs Genemark
 Returns :   A Bio::Tools::Genemark object
 Args    :   An array of Bio::PrimarySeqI objects

_run

 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)

_write_seq_file

 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