Fugassem

* Added option for hyperparameter tuning RF

* Renamed options for '--go-mode'
* Added 'bypass-coexp' option to skip calculating coexpression
* Fixed issue when using '--bypass-prediction' option
* Added options for calculating feature vector

* Reorganize output folders
* Added a finalized combined results file
* Added stratified option for 'Terminal' or 'Strain' level
* Fixed issue when filtering based on prevalence
* Fixed issue when merging results

* Added option for prediction using universal GO set
* Added option for prediction using global GO set
* Added option for predicting terms from all GO ontologies
* Refined generate_annotation_input module to prepare co-homology evidence
* Added function for visualization
* Fixed issue on processing fugassem_stratified_abundance module
* Added example data

* Fixed small issue from geneontology.py
* Added function for detailed annotation when '--go-level none'
* Tweaked stratified_abundance.py for accepting compressed input files
* Added format_function module for formatting input file
* Fixed issue when using different zero-filtering approach