def test_newick_default_values(self):
parser = cli.get_msp_parser()
cmd = "newick"
history_file = "test3.hdf5"
args = parser.parse_args([cmd, history_file])
self.assertEqual(args.history_file, history_file)
self.assertEqual(args.precision, 3)
def test_mutations_default_values(self):
parser = cli.get_msp_parser()
cmd = "mutations"
history_file = "test.hdf5"
args = parser.parse_args([cmd, history_file])
self.assertEqual(args.history_file, history_file)
self.assertEqual(args.header, False)
def test_newick_long_args(self):
parser = cli.get_msp_parser()
cmd = "newick"
history_file = "test.hdf5"
args = parser.parse_args([
cmd, history_file, "--precision=5"])
self.assertEqual(args.history_file, history_file)
self.assertEqual(args.precision, 5)
def test_newick_short_args(self):
parser = cli.get_msp_parser()
cmd = "newick"
history_file = "test.hdf5"
args = parser.parse_args([
cmd, history_file, "-p", "10"])
self.assertEqual(args.history_file, history_file)
self.assertEqual(args.precision, 10)
def test_mutations_long_args(self):
parser = cli.get_msp_parser()
cmd = "mutations"
history_file = "test.hdf5"
args = parser.parse_args([
cmd, history_file, "--header"])
self.assertEqual(args.history_file, history_file)
self.assertEqual(args.header, True)
def test_records_short_args(self):
parser = cli.get_msp_parser()
cmd = "records"
history_file = "test.hdf5"
args = parser.parse_args([
cmd, history_file, "-H"])
self.assertEqual(args.history_file, history_file)
self.assertEqual(args.header, True)
def test_simulate_default_values(self):
parser = cli.get_msp_parser()
cmd = "simulate"
args = parser.parse_args([cmd, "10", "out.hdf5"])
self.assertEqual(args.sample_size, 10)
self.assertEqual(args.history_file, "out.hdf5")
self.assertEqual(args.recombination_rate, 0.0)
self.assertEqual(args.mutation_rate, 0.0)
self.assertEqual(args.num_loci, 1)
self.assertEqual(args.random_seed, None)
self.assertEqual(args.max_memory, "1G")
self.assertEqual(args.compress, False)
def test_simulate_short_args(self):
parser = cli.get_msp_parser()
cmd = "simulate"
args = parser.parse_args([
cmd, "100", "out2.hdf5", "-m", "1e3", "-r", "5", "-u", "2",
"-s", "1234", "-M", "2G", "-z"])
self.assertEqual(args.sample_size, 100)
self.assertEqual(args.history_file, "out2.hdf5")
self.assertEqual(args.recombination_rate, 5)
self.assertEqual(args.num_loci, 1000)
self.assertEqual(args.random_seed, 1234)
self.assertEqual(args.max_memory, "2G")
self.assertEqual(args.compress, True)
def test_simulate_long_args(self):
parser = cli.get_msp_parser()
cmd = "simulate"
args = parser.parse_args([
cmd, "1000", "out3.hdf5",
"--num-loci", "1e4",
"--recombination-rate", "6",
"--mutation-rate", "1",
"--random-seed", "123",
"--max-memory", "20M",
"--compress"])
self.assertEqual(args.sample_size, 1000)
self.assertEqual(args.history_file, "out3.hdf5")
self.assertEqual(args.recombination_rate, 6)
self.assertEqual(args.num_loci, 10000)
self.assertEqual(args.random_seed, 123)
self.assertEqual(args.max_memory, "20M")
self.assertEqual(args.compress, True)
def test_macs_default_values(self):
parser = cli.get_msp_parser()
cmd = "macs"
history_file = "test2.hdf5"
args = parser.parse_args([cmd, history_file])
self.assertEqual(args.history_file, history_file)