Bio::Tools::Glimmer - parser for GlimmerM/GlimmerHMM eukaryotic gene predictions
use Bio::Tools::Glimmer; my $parser = new Bio::Tools::Glimmer(-file => $file); # filehandle: $parser = Bio::Tools::Glimmer->new( -fh => \*INPUT ); # 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()) { # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits # off Bio::SeqFeature::Gene::Transcript. # # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @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'); }
This is a module for parsing 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.
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/.
This module does not parse Glimmer2 or Glimmer3 bacterial gene prediction files. Details on their output formats can be found at http://www.cbcb.umd.edu/software/glimmer/.
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Torsten Seemann
Mark Johnson
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Tools::Glimmer(); Function: Builds a new Bio::Tools::Glimmer object Returns : an instance of Bio::Tools::Glimmer Args :
Usage : $glimmer->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /glimmer/i. Returns : String Argument : n/a
Title : next_feature Usage : while($gene = $glimmer->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Glimmer result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args :
Title : next_prediction Usage : while($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 :
Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns :
Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns :
Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns :
Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.