Bio::Tools::Run::Glimmer man page on Pidora

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Bio::Tools::Run::GlimmUser)Contributed Perl DocumenBio::Tools::Run::Glimmer(3)

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://bugzilla.open-bio.org/

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 v5.14.1			  2011-07-21	   Bio::Tools::Run::Glimmer(3)
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