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: mjohnson-at-watson-dot-wustl-dot-edu

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