def test_get_subs_matrix_incomplete(self):
# Ensure understandable exception is raised when a WT/var
# combo is absent from the data.
d = load_dataset("test/data_incomplete.txt")
self.assertRaises(AssertionError, get_subs_matrix, d)
def test_get_subs_matrix(self):
d = load_dataset("test/data.txt")
mat = get_subs_matrix(d)
self.assertEqual(len(mat), 400)
def test_load_dataset_col_names(self):
# Ensure custom column names can be specified.
d1 = load_dataset("test/data.txt")
d2 = load_dataset("test/data_colnames.txt",
cols=["Position", "wt", "Mutant", "fitness"])
self.assertEqual(d1, d2)
def test_load_dataset_filtering(self):
# Ensure synonymous variants and those with non-canonical WT
# or variant AAs are ignored.
d = load_dataset("test/data.txt")
self.assertEqual(len(d), 380)
def test_load_dataset_col_order(self):
# Ensure data cols can be in any order.
d1 = load_dataset("test/data.txt")
d2 = load_dataset("test/data_order.txt")
self.assertEqual(d1, d2)