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)