--- name: "Bio::Tools::Glimmer" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Glimmer" --- # Bio::Tools::Glimmer(3pm) parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions ## NAME Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions ## SYNOPSIS ``` use Bio::Tools::Glimmer; # file my $parser = Bio::Tools::Glimmer->new(-file => $file); # filehandle: $parser = Bio::Tools::Glimmer->new( -fh => \*INPUT ); # provide a sequence identifier (Glimmer 2.X) my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname); # force format (override automatic detection) my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM'); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same while(my $gene = $parser->next_prediction()) { # For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance # of Bio::Tools::Prediction::Gene, which inherits off # Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an # array of Bio::Tools::Prediction::Exon objects. # For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an # instance of Bio::SeqFeature::Generic # all exons (eukaryotic only): @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); } ``` ## DESCRIPTION This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions. It will create gene objects from the prediction report which can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for use with Gbrowse. Glimmer is open source and available at \. GlimmerM is open source and available at \. GlimmerHMM is open source and available at \. Note that Glimmer 2.X will only process the first sequence in a fasta file, and the prediction report does not contain any sort of sequence identifier Note that Glimmer 3.X produces two output files. This module only parses the .predict file. ## 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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via email or the web: ``` https://github.com/bioperl/bioperl-live/issues ``` ## AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org ## CONTRIBUTORS Torsten Seemann Mark Johnson ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### new ``` Title : new Usage : my $obj = Bio::Tools::Glimmer->new(); Function: Builds a new Bio::Tools::Glimmer object Returns : an instance of Bio::Tools::Glimmer Args : format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname ``` ### analysis\_method ``` Usage : $glimmer->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /glimmer/i. Returns : String Argument : n/a ``` ### next\_feature ``` Title : next_feature Usage : while($gene = $glimmer->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Glimmer result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : ``` ### next\_prediction ``` Title : next_prediction Usage : while($gene = $glimmer->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Glimmer result file. Call this method repeatedly until FALSE is returned. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : ``` ### \_parse\_predictions ``` Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : ``` ### \_parse\_eukaryotic ``` Title : _parse_eukaryotic() Usage : $obj->_parse_eukaryotic() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : ``` ### \_parse\_prokaryotic ``` Title : _parse_prokaryotic() Usage : $obj->_parse_prokaryotic() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : ``` ### \_prediction ``` Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : ``` ### \_add\_prediction ``` Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : ``` ### \_predictions\_parsed ``` Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE ``` ### \_seqname ``` Title : _seqname Usage : $obj->_seqname($seqname) Function: internal (for Glimmer 2.X) Example : Returns : String ``` ### \_seqlength ``` Title : _seqlength Usage : $obj->_seqlength($seqlength) Function: internal (for Glimmer 2.X) Example : Returns : String ``` ### \_format ``` Title : _format Usage : $obj->_format($format) Function: internal Example : Returns : String ``` ### \_detail\_file ``` Title : _detail_file Usage : $obj->_detail_file($filename) Function: internal (for Glimmer 3.X) Example : Returns : String ```