def test_operation_eq(self):
a = PopulationSizeVariable("a")
b = PopulationSizeVariable("b")
comb1 = operation_creation(Addition, a, b)
comb2 = operation_creation(Addition, b, a)
self.assertEqual(comb1, comb1)
self.assertEqual(comb2, comb2)
self.assertEqual(comb1, comb2)
comb2 = operation_creation(Addition, a, b)
self.assertEqual(comb1, comb2)
c = TimeVariable("c")
comb1 = Addition(c, Multiplication(a, b))
comb2 = Addition(Multiplication(b, a), c)
self.assertEqual(comb1, comb2)
self.assertNotEqual(Division(a, b), Division(b, a))
self.assertNotEqual(Subtraction(a, b), Subtraction(b, a))
self.assertEqual(Addition(a, b), Addition(b, a))
self.assertEqual(Multiplication(a, b), Multiplication(b, a))
self.assertEqual(Exp(a), Exp(a))
self.assertNotEqual(Exp(b), Exp(a))
self.assertNotEqual(Log(b), Exp(b))
self.assertNotEqual(Log(b), Multiplication(a, b))
self.assertEqual(Exp(Multiplication(a, b)), Exp(Multiplication(b, a)))
def test_translation_from_epoch_to_tree3(self):
N_a, nu1B, nu1, nu1F, nu2B, nu2F, t1, t2, t3 = self.get_genetic_variables_model3(
)
var2values = {
'N_a': 1e5,
'nu1B': 0.4,
'nu1': 0.8,
'nu1F': 0.1,
'nu2B': 0.2,
'nu2F': 0.5,
't1': 2,
't2': 4,
't3': 5
}
cm = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
cm.add_leaf(0, size_pop=nu1F)
cm.add_leaf(1, size_pop=nu2F)
cm.change_pop_size(0, t=t1, size_pop=nu1)
cm.change_pop_size(0, t=t2, size_pop=nu1B)
cm.change_pop_size(1, t=t1, size_pop=nu2B)
cm.move_lineages(1, 0, t=t3, size_pop=N_a)
em = EpochDemographicModel(gen_time=29,
Nanc_size=N_a,
mutation_rate=1.25e-8)
em.add_split(0, [nu1B, nu2B])
em.add_epoch(operation_creation(Subtraction, t3, t2), [nu1B, nu2B])
em.add_epoch(operation_creation(Subtraction, t2, t1), [nu1, nu2B])
em.add_epoch(operation_creation(Subtraction, t1, 0), [nu1F, nu2F])
translated_model, _ = em.translate_to(TreeDemographicModel, var2values)
self.assertTrue(translated_model.equals(cm, var2values))
def test_creation_log(self):
a = PopulationSizeVariable("a")
b = PopulationSizeVariable("b")
l1 = operation_creation(Log, a)
self.assertIsInstance(l1, Log)
exp_b = Exp(b)
self.assertEqual(operation_creation(Log, exp_b), b)
self.assertEqual(operation_creation(Log, 1), 0)
self.assertRaises(ValueError, operation_creation, Log, 0, 0)
def test_creation_exp(self):
a = PopulationSizeVariable("a")
b = PopulationSizeVariable("b")
e1 = operation_creation(Exp, a)
self.assertIsInstance(e1, Exp)
log_b = Log(b)
self.assertEqual(operation_creation(Exp, log_b), b)
self.assertEqual(operation_creation(Exp, 0), 1)
self.assertRaises(ValueError, operation_creation, Exp, 0, 0)
def test_creation_division(self):
a = PopulationSizeVariable("a")
b = PopulationSizeVariable("b")
self.assertEqual(operation_creation(Division, 8, 2), 4)
self.assertEqual(operation_creation(Division, a, 1), a)
self.assertRaises(ValueError, operation_creation, Division, a, 0)
self.assertEqual(operation_creation(Division, b, b), 1)
self.assertRaises(ValueError, operation_creation, Division, a)
def test_translation_from_epoch_to_tree1(self):
from .test_tree_dem_model import TestTreeDemModel
N_a, nu1, nu2, nu2F, t1, t2 = TestTreeDemModel.get_genetic_variables_model1(
)
var2values = {
'nu1': 0.4,
'nu2F': 0.7,
'nu2': 0.5,
'N_a': 1e5,
't1': 1,
't2': 5
}
em = EpochDemographicModel(gen_time=29,
Nanc_size=N_a,
mutation_rate=1.25e-8)
em.add_split(0, [nu1, nu2])
em.add_epoch(operation_creation(Subtraction, t2, t1), [nu1, nu2])
em.add_epoch(operation_creation(Subtraction, t1, 0), [nu1, nu2F])
cm = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
cm.add_leaf(0, size_pop=nu1)
cm.add_leaf(1, size_pop=nu2F)
cm.change_pop_size(1, t=t1, size_pop=nu2)
cm.move_lineages(1, 0, t=t2, size_pop=N_a)
translated_model, _ = em.translate_to(TreeDemographicModel, var2values)
self.assertTrue(translated_model.equals(cm, var2values))
# fails
self.assertRaises(ValueError, EpochDemographicModel.create_from, cm)
self.assertRaises(ValueError, TreeDemographicModel.create_from,
cm.events[0], None)
tm = TreeDemographicModel()
self.assertRaises(ValueError, tm.translate_to, EpochDemographicModel,
[])
self.assertRaises(ValueError, tm.translate_to, Epoch, [])
def test_creation_add(self):
a = PopulationSizeVariable("a")
b = PopulationSizeVariable("b")
self.assertEqual(operation_creation(Addition, 0, 1), 1)
self.assertEqual(operation_creation(Addition, a, 0), a)
self.assertEqual(operation_creation(Addition, 0, b), b)
self.assertIsInstance(operation_creation(Addition, a, 1), Addition)
self.assertIsInstance(operation_creation(Addition, 1, b), Addition)
self.assertIsInstance(operation_creation(Addition, a, b), Addition)
self.assertRaises(ValueError, operation_creation, Addition, 0)
def test_creation_subtract(self):
a = PopulationSizeVariable("a")
b = PopulationSizeVariable("b")
self.assertEqual(operation_creation(Subtraction, 1, 0), 1)
self.assertEqual(operation_creation(Subtraction, a, 0), a)
# (1 + a * b) - ((b * a) + 1) = 0
self.assertEqual(
operation_creation(
Subtraction,
operation_creation(Addition, 1,
operation_creation(Multiplication, a, b)),
operation_creation(Addition,
operation_creation(Multiplication, b, a),
1)), 0)
self.assertRaises(ValueError, operation_creation, Subtraction, 0)
def test_creation_multiplication(self):
a = PopulationSizeVariable("a")
b = PopulationSizeVariable("b")
self.assertEqual(operation_creation(Multiplication, 2, 4), 8)
self.assertEqual(operation_creation(Multiplication, 1, a), a)
self.assertEqual(operation_creation(Multiplication, a, 1), a)
self.assertEqual(operation_creation(Multiplication, 0, b), 0)
self.assertEqual(operation_creation(Multiplication, b, 0), 0)
self.assertIsInstance(operation_creation(Multiplication, a, b),
Multiplication)
self.assertRaises(ValueError, operation_creation, Multiplication, a)