Bio::Tools::Run::Glimmer.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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