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)
