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.
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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