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)