Bio::Tools::Run::Genemark(3pm)				User Contributed Perl Documentation			    Bio::Tools::Run::Genemark(3pm)

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

perl v5.12.3							    2011-06-18					    Bio::Tools::Run::Genemark(3pm)