associations = GeneAssociations.fromFile(associationsFileName, taxons=TAXONS, dataset=dataset) #reservedAssociations = GeneAssociations.fromFile(associationsFileName+"_reserved", dataset = reserved) ontology.setAssociations(associations) #ontology.setAssociations(reservedAssociations, 'reserved') if options.associationsDump: associations.serialize(options.associationsDump) #reservedAssociations.serialize(options.associationsDump+"_reserved") sys.exit() ontology.deleteSmallTerms(options.lb) associations.shrink(options.max, options.lb) ontology.overView() ontology.dotExport() #ontology._toBayessNet(None,None) TreeLikerWrapper.maxMemory = options.memory Gene.recalculateDists = bool(options.recalcDists) if options.sampling: sample_size, samples = options.sampling.split("x") else: sample_size, samples = options.max, 1 treelikerArgs = (options.treeliker, options.template, sample_size, samples) ontology.completeTest(treelikerArgs, options.processes)
#dataset = set(dataset[splitIndex:]) dataset = set(dataset) associations = GeneAssociations.fromFile(associationsFileName, taxons = TAXONS, dataset = dataset) #reservedAssociations = GeneAssociations.fromFile(associationsFileName+"_reserved", dataset = reserved) ontology.setAssociations(associations) #ontology.setAssociations(reservedAssociations, 'reserved') if options.associationsDump: associations.serialize(options.associationsDump) #reservedAssociations.serialize(options.associationsDump+"_reserved") sys.exit() ontology.deleteSmallTerms(options.lb) associations.shrink(options.max, options.lb) ontology.overView() ontology.dotExport() #ontology._toBayessNet(None,None) TreeLikerWrapper.maxMemory = options.memory Gene.recalculateDists = bool(options.recalcDists) if options.sampling: sample_size, samples = options.sampling.split("x") else: sample_size, samples = options.max, 1 treelikerArgs = (options.treeliker, options.template, sample_size, samples) ontology.completeTest(treelikerArgs, options.processes)