Provided by: libbio-perl-run-perl_1.7.3-3_all
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.
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. firstname.lastname@example.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: email@example.com 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
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