/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Glimmer

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: johnsonm-at-gmail-dot-com

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