def main(args):
filename = args.file
method = args.method
print("-STARTING-\n")
print("Using")
print("Ab cutoff: {}".format(args.ab_count_cutoff))
print("Culture cutoff: {}".format(args.culture_cutoff))
print("Method: {}".format(method))
print("Analysis type: {}".format(args.analysis_type))
print()
if args.average:
classifier = average.Average(filename,
CULTURE_SIZE_CUTOFF=args.culture_cutoff,
AB_CULTURE_COUNT_CUTOFF=args.ab_count_cutoff,
ESBL_AB_RESISTENCE_LIST=ESBL_AB_RESISTANCE_LIST,
RELEVANT_MO_LIST=RELEVANT_MO_LIST)
# elif args.svm:
# SVM.run(filename, args.culture_cutoff, args.ab_count_cutoff, ESBL_AB_RESISTANCE_LIST)
elif args.tree:
classifier = decision_tree.DecisionTree(filename,
CULTURE_SIZE_CUTOFF=args.culture_cutoff,
AB_CULTURE_COUNT_CUTOFF=args.ab_count_cutoff,
ESBL_AB_RESISTANCE_LIST=ESBL_AB_RESISTANCE_LIST,
RELEVANT_MO_LIST=RELEVANT_MO_LIST,
testmode=method,
analysis_type=args.analysis_type,
medication_file=args.medication_file)
elif args.perceptron:
classifier = perceptron.Perceptron(filename,
CULTURE_SIZE_CUTOFF=args.culture_cutoff,
AB_CULTURE_COUNT_CUTOFF=args.ab_count_cutoff,
ESBL_AB_RESISTANCE_LIST=ESBL_AB_RESISTANCE_LIST,
RELEVANT_MO_LIST=RELEVANT_MO_LIST,
testmode=method,
analysis_type=args.analysis_type,
medication_file=args.medication_file)
classifier.run()
def test_average2(self):
self.assertEqual(average.Average([0, 1]), 0.5)
def test_average4(self):
self.assertEqual(average.Average([]), None)
def test_average1(self):
self.assertEqual(average.Average([1, 2, 3, 4, 5, 6, 7]), 4)
def test_average_2(self):
self.assertEqual(average.Average([1, 2, 3]), 2)
def test_average3(self):
self.assertEqual(average.Average([1, 2, 3, 'l']), None)
def test_average_1(self):
self.assertEqual(average.Average([1, 2, 3, 4, 5]), 3)
def test_average_5(self):
self.assertEqual(average.Average("Hello"), "Something")
def test_average_4(self):
self.assertEqual(average.Average("I am a string"), None)
def test_average_3b(self):
self.assertEqual(average.Average([]), -1)
def test_average_3a(self):
self.assertEqual(average.Average(['a', 'b', 'c']), None)
