tigr-glimmer(1) [debian man page]

TIGR-GLIMMER(1) 					      General Commands Manual						   TIGR-GLIMMER(1)

NAME

       tigr-glimmer - runs various programs of the TIGR Glimmer suite

SYNOPSIS

       tigr-glimmer program [arguments]

DESCRIPTION

       This  manual  page  documents  briefly  the tigr-glimmer wrapper to the TIGR Glimmer programs.  This manual page was written for the Debian
       GNU/Linux distribution because upstream does not provide this wrapper and it was invented for Debian to avoid conflicts with other packages
       that might cause a name space polution.

       tigr-glimmer is just a wrapper that invokes the various programs in the TIGR Glimmer software package. You can get more detailed documenta-
       tion in /usr/share/doc/tigr-glimmer.  Please note that the documentation there is a part of the former  version	Glimmer  2.   The  version
       Glimmer 3 has some features that were described in the notes.pdf document inside the documentation directory.

       The  following programs are included: anomaly, build-fixed, build-icm, entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-
       extract, score-fixed, start-codon-distrib, test, uncovered and window-acgt.

OPTIONS

       There are no options.

EXAMPLES

       tigr-glimmer build-icm

       tigr-glimmer long-orfs

SEE ALSO

       For the pre previously packaged version Glimmer2 some text files from the documentation were turned to man pages for the  Debian  GNU/Linux
       distribution by Steffen Moeller <moeller@debian.org>

AUTHORS

       This manual page was written by Andreas Tille <tille@debian.org>, for the Debian GNU/Linux system (but may be used by others).

								  April 16, 2008						   TIGR-GLIMMER(1)

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

NAME

       Bio::Tools::Run::Glimmer - Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.

SYNOPSIS

	 # glimmer2
	 my $factory =
	     Bio::Tools::Run::Glimmer->new('-program' => 'glimmer3',
					   '-model'   => 'model.icm');
	 # glimmer3
	 my $factory =
	     Bio::Tools::Run::Glimmer->new('-program' => 'glimmer2',
					   '-model'   => 'model.icm');
	 # glimmerm
	 my $factory =
	     Bio::Tools::Run::Glimmer->new('-program' => 'glimmerm');

	 # glimmerHMM
	 my $factory =
	     Bio::Tools::Run::Glimmer->new('-program' => 'glimmerHMM');

	 # Pass the factory Bio::Seq objects
	 # returns a Bio::Tools::Glimmer object
	 my $glimmer = $factory->run($seq);
	 or
	 my $glimmer = $factor->run(@seq);

DESCRIPTION

       Wrapper module for the Glimmer family of programs.  Should work with all currently available flavors: Glimmer, GlimmerM and GlimmerHMM.
       However, only Glimmer 2.X and 3.X have been tested.

       Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>.

       GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>.

       GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>.

       Note that Glimmer 2.X 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).

       Note that Glimmer 3.X produces two output files.  This module only passes the .predict file to Bio::Tools::Glimmer.

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

   model
	Title	: model
	Usage	: $factory>model()
	Function: gets/sets the name of the model (icm) file
	Returns:  string
	Args	: string

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

   run
	Title	:   run
	Usage	:   $obj->run($seq_file)
	Function:   Runs Glimmer/GlimmerM/GlimmerHMM
	Returns :   A Bio::Tools::Glimmer 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::Glimmer
	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::Glimmer(3pm)