def test_epsilon(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output, "-e", "123"])
self.assertEqual(args.epsilon, 123)
args = parser.parse_args(
[self.infile, self.output, "--epsilon", "321"])
self.assertEqual(args.epsilon, 321)
def test_time_grid(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output, "-g", "adaptive"])
self.assertEqual(args.time_grid, "adaptive")
args = parser.parse_args(
[self.infile, self.output, "--time-grid", "uniform"])
self.assertEqual(args.time_grid, "uniform")
def test_recombination_rate(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output, "-r", "1e-100"])
self.assertEqual(args.recombination_rate, 1e-100)
args = parser.parse_args(
[self.infile, self.output, "--recombination-rate", "1e-100"])
self.assertEqual(args.recombination_rate, 1e-100)
def test_mutation_rate(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output, "-m", "1e10"])
self.assertEqual(args.mutation_rate, 1e10)
args = parser.parse_args(
[self.infile, self.output, "--mutation-rate", "1e10"])
self.assertEqual(args.mutation_rate, 1e10)
def test_num_threads(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args(
[self.infile, self.output, "10000", "--num-threads", "1"])
self.assertEqual(args.num_threads, 1)
args = parser.parse_args(
[self.infile, self.output, "10000", "--num-threads", "2"])
self.assertEqual(args.num_threads, 2)
def test_method(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args(
[self.infile, self.output, "10000", "--method", "inside_outside"])
self.assertEqual(args.method, "inside_outside")
args = parser.parse_args(
[self.infile, self.output, "10000", "--method", "maximization"])
self.assertEqual(args.method, "maximization")
def test_probability_space(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args(["date", self.infile, self.output, "10000",
"--probability-space", "linear"])
self.assertEqual(args.probability_space, "linear")
args = parser.parse_args(["date", self.infile, self.output, "10000",
"--probability-space", "logarithmic"])
self.assertEqual(args.probability_space, "logarithmic")
def test_default_values_preprocess(self):
with mock.patch("tsdate.cli.setup_logging"):
parser = cli.tsdate_cli_parser()
args = parser.parse_args(["preprocess", self.infile, self.output])
self.assertEqual(args.tree_sequence, self.infile)
self.assertEqual(args.output, self.output)
self.assertEqual(args.minimum_gap, 1000000)
self.assertTrue(args.trim_telomeres)
def test_default_values(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output])
self.assertEqual(args.ts, self.infile)
self.assertEqual(args.output, self.output)
self.assertEqual(args.Ne, 10000)
self.assertEqual(args.time_grid, "adaptive")
self.assertEqual(args.mutation_rate, None)
self.assertEqual(args.recombination_rate, None)
self.assertEqual(args.slices, 50)
self.assertEqual(args.epsilon, 1e-6)
self.assertEqual(args.num_threads, 0)
self.assertFalse(args.progress)
def test_default_values(self):
with mock.patch("tsdate.cli.setup_logging"):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output, "1"])
self.assertEqual(args.ts, self.infile)
self.assertEqual(args.output, self.output)
self.assertEqual(args.Ne, 1)
self.assertEqual(args.mutation_rate, None)
self.assertEqual(args.recombination_rate, None)
self.assertEqual(args.epsilon, 1e-6)
self.assertEqual(args.num_threads, None)
self.assertEqual(args.probability_space, 'logarithmic')
self.assertEqual(args.method, 'inside_outside')
self.assertFalse(args.progress)
def test_progress(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args(
[self.infile, self.output, "10000", "--progress"])
self.assertTrue(args.progress)
def test_Ne(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output, "-n", "10000"])
self.assertEqual(args.Ne, 10000)
args = parser.parse_args([self.infile, self.output, "--Ne", "10000"])
self.assertEqual(args.Ne, 10000)
def test_slices(self):
parser = cli.tsdate_cli_parser()
args = parser.parse_args([self.infile, self.output, "-s", "100"])
self.assertEqual(args.slices, 100)
args = parser.parse_args([self.infile, self.output, "--slices", "100"])
self.assertEqual(args.slices, 100)
