Provided by: libbio-perl-run-perl_1.7.3-3_all bug


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


         # 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 <>.

       Contact information for licensing inquiries is available at:

       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


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AUTHOR - Mark Johnson

        Email: johnsonm-at-gmail-dot-com


       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