def test_size_events(self):
parser = cli.get_mspms_parser()
args = parser.parse_args(["40", "20"])
self.assertEqual(args.size_event, [])
args = parser.parse_args("10 1 -eN 2.0 0.5".split())
self.assertEqual(args.size_event, [[2.0, 0.5]])
args = parser.parse_args("10 1 -eN 2.0 0.5 -eN 1.0 5.0".split())
self.assertEqual(args.size_event, [[2.0, 0.5], [1.0, 5.0]])
def test_trees(self):
parser = cli.get_mspms_parser()
args = parser.parse_args(["40", "20"])
self.assertEqual(args.trees, False)
args = parser.parse_args(["40", "20", "-T"])
self.assertEqual(args.trees, True)
args = parser.parse_args(["40", "20", "--trees"])
self.assertEqual(args.trees, True)
def test_mutations(self):
parser = cli.get_mspms_parser()
args = parser.parse_args(["40", "20"])
self.assertEqual(args.mutation_rate, 0.0)
args = parser.parse_args(["40", "20", "-t", "10"])
self.assertEqual(args.mutation_rate, 10.0)
args = parser.parse_args(["40", "20", "--mutation-rate=10"])
self.assertEqual(args.mutation_rate, 10.0)
def test_growth_rates(self):
parser = cli.get_mspms_parser()
args = parser.parse_args(["40", "20"])
self.assertEqual(args.growth_rate, None)
self.assertEqual(args.growth_event, [])
args = parser.parse_args("15 1000 -G 5.25".split())
self.assertEqual(args.growth_rate, 5.25)
self.assertEqual(args.growth_event, [])
args = parser.parse_args("15 1000 -eG 1.0 5.25".split())
self.assertEqual(args.growth_rate, None)
self.assertEqual(args.growth_event, [[1.0, 5.25]])
args = parser.parse_args("15 1000 -eG 1.0 5.25 -eG 2.0 10".split())
self.assertEqual(args.growth_rate, None)
self.assertEqual(args.growth_event, [[1.0, 5.25], [2.0, 10.0]])
args = parser.parse_args(
"15 1000 -eG 1.0 5.25 -eG 2.0 10 -G 4".split())
self.assertEqual(args.growth_rate, 4.0)
self.assertEqual(args.growth_event, [[1.0, 5.25], [2.0, 10.0]])
def test_msdoc_examples(self):
parser = cli.get_mspms_parser()
args = parser.parse_args(["4", "2", "-t", "5.0"])
self.assertEqual(args.sample_size, 4)
self.assertEqual(args.num_replicates, 2)
self.assertEqual(args.mutation_rate, 5.0)
self.assertEqual(args.trees, False)
args = parser.parse_args(["4", "2", "-T"])
self.assertEqual(args.sample_size, 4)
self.assertEqual(args.num_replicates, 2)
self.assertEqual(args.mutation_rate, 0.0)
self.assertEqual(args.trees, True)
args = parser.parse_args("15 1000 -t 10.04 -r 100.0 2501".split())
self.assertEqual(args.sample_size, 15)
self.assertEqual(args.num_replicates, 1000)
self.assertEqual(args.mutation_rate, 10.04)
self.assertEqual(args.trees, False)
self.assertEqual(args.recombination, [100, 2501])
args = parser.parse_args(
"15 1000 -t 2.0 -eN 1.0 .1 -eN 2.0 4.0".split())
self.assertEqual(args.sample_size, 15)
self.assertEqual(args.num_replicates, 1000)
self.assertEqual(args.mutation_rate, 2.0)
self.assertEqual(args.size_event, [[1.0, 0.1], [2.0, 4.0]])
args = parser.parse_args(
"15 1000 -t 6.4 -G 6.93 -eG 0.2 0.0 -eN 0.3 0.5".split())
self.assertEqual(args.sample_size, 15)
self.assertEqual(args.num_replicates, 1000)
self.assertEqual(args.mutation_rate, 6.4)
self.assertEqual(args.growth_rate, 6.93)
self.assertEqual(args.growth_event, [[0.2, 0.0]])
self.assertEqual(args.size_event, [[0.3, 0.5]])
def test_positional_arguments(self):
parser = cli.get_mspms_parser()
args = parser.parse_args(["40", "20"])
self.assertEqual(args.sample_size, 40)
self.assertEqual(args.num_replicates, 20)
