| Bio::Tools::Run::Glimmer(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Glimmer(3pm) |
Bio::Tools::Run::Glimmer - Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.
# 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);
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.
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
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.
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/
Email: johnsonm-at-gmail-dot-com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: gets/sets the program name Returns: string Args : string
Title : program_dir Usage : $factory->program_dir() Function: gets/sets the program dir Returns: string Args : string
Title : model Usage : $factory>model() Function: gets/sets the name of the model (icm) file Returns: string Args : string
Title : new Usage : $glimmer->new(@params) Function: creates a new Glimmer factory Returns: Bio::Tools::Run::Glimmer Args :
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
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An instance of Bio::Tools::Glimmer Args : file name, sequence identifier (optional)
Title : _write_seq_file Usage : obj->_write_seq_file($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
| 2023-01-22 | perl v5.36.0 |