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_models_eq(self):
# it does not check everything
var1 = PopulationSizeVariable("nu")
epoch1 = Epoch(init_size_args=[1, 2], size_args=[var1, 5], time_arg=10)
epoch2 = copy.copy(epoch1)
self.assertEqual(epoch1, epoch1)
self.assertEqual(epoch1, epoch2)
epoch1.size_args = [4, 5]
self.assertNotEqual(epoch1, epoch2)
epoch1.size_args = [var1, 5]
epoch1.dyn_args = ["Sud", "Sud"]
self.assertEqual(epoch1, epoch2)
epoch1.dyn_args = ["Sud", "Exp"]
self.assertNotEqual(epoch1, epoch2)
split = Split(pop_to_div=0, size_args=[1, 2])
self.assertNotEqual(epoch1, split)
self.assertNotEqual(split, epoch1)
self.assertEqual(split, split)
pop_change1 = PopulationSizeChange(pop=0, t=10)
pop_change2 = PopulationSizeChange(pop=1, t=10)
self.assertEqual(pop_change1, pop_change1)
self.assertTrue(pop_change1.equals(pop_change1, []))
self.assertNotEqual(pop_change1, pop_change2)
lin_move1 = LineageMovement(pop_from=0, pop=1, t=10)
lin_move2 = LineageMovement(pop_from=1, pop=0, t=10)
self.assertEqual(lin_move1, lin_move1)
self.assertTrue(lin_move1.equals(lin_move1, []))
self.assertNotEqual(lin_move1, lin_move2)
model1 = EpochDemographicModel()
self.assertEqual(model1, model1)
self.assertNotEqual(model1, split)
model2 = EpochDemographicModel()
model2.add_epoch(time_arg=10, size_args=[1])
self.assertNotEqual(model1, model2)
model1.add_epoch(time_arg=10, size_args=[2])
self.assertNotEqual(model1, model2)
model1 = TreeDemographicModel()
self.assertEqual(model1, model1)
self.assertTrue(model1.equals(model1, []))
self.assertNotEqual(model1, split)
self.assertFalse(model1.equals(split, []))
model2 = TreeDemographicModel()
model2.add_leaf(pop=0, size_pop=10)
self.assertNotEqual(model1, model2)
self.assertFalse(model1.equals(model2, []))
model1.add_leaf(pop=1, size_pop=11)
self.assertNotEqual(model1, model2)
model2.add_leaf(pop=1, size_pop=11)
model1.add_leaf(pop=0, size_pop=10)
self.assertEqual(model1, model2)
def test_model2_translation(self):
N_a, nu1, nu2, nu2F, t1, t2 = self.get_genetic_variables_model1()
var2values = {
'nu1': 0.4,
'nu2F': 0.7,
'nu2': 0.5,
'N_a': 1e5,
't1': 1,
't2': 5
}
m = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
m.add_leaf(0, size_pop=nu1)
m.add_leaf(1, size_pop=nu2F)
m.change_pop_size(1, t=t1, size_pop=nu2, dyn="Exp", g=0.9)
m.move_lineages(1, 0, t=t2, size_pop=N_a)
em = EpochDemographicModel(gen_time=29, mutation_rate=1.25e-8)
# g = log(N / N0) / t where N is final size (closer to nowdays) and
# N0 is start size (the most ancient) t - time interval
# THEN we have g, t and N and we want N0 = N / exp(gt)
exp_op = operation_creation(
Exp,
operation_creation(Multiplication, 0.9,
operation_creation(Subtraction, t2, t1)))
nu20 = operation_creation(Division, nu2, exp_op)
# Construct our model
em.add_split(0, [nu1, nu20])
em.add_epoch(operation_creation(Subtraction, t2, t1), [nu1, nu2],
dyn_args=['Sud', "Exp"])
em.add_epoch(operation_creation(Subtraction, t1, 0), [nu1, nu2F])
translated_model = m.translate_to(EpochDemographicModel, var2values)
def test_model1_translation(self):
N_a, nu1, nu2, nu2F, t1, t2 = self.get_genetic_variables_model1()
var2values = {
'nu1': 0.4,
'nu2F': 0.7,
'nu2': 0.5,
'N_a': 1e5,
't1': 1,
't2': 5
}
m = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
m.add_leaf(0, size_pop=nu1)
m.add_leaf(1, size_pop=nu2F)
m.change_pop_size(1, t=t1, size_pop=nu2)
m.move_lineages(1, 0, t=t2, size_pop=N_a)
self.assertEqual(m.number_of_populations(), 2)
translated_model = EpochDemographicModel.create_from(m, var2values)
em = EpochDemographicModel(gen_time=29, 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])
self.assertEqual(translated_model, em)
def test_model5_translation(self):
N_a, nu1B, nu1, nu1F, nu2B, nu2F, t1, t2, t3 = self.get_genetic_variables_model3(
)
t4 = TimeVariable('t4', units="genetic")
var2values = {
'N_a': 1e5,
'nu1B': 0.4,
'nu1': 0.8,
'nu1F': 0.1,
'nu2B': 0.5,
'nu2F': 0.2,
't1': 2,
't2': 3,
't3': 4,
't4': 5
}
m = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
m.add_leaf(0, size_pop=nu1F)
m.add_leaf(1, size_pop=nu2F)
m.change_pop_size(0, t=t1, size_pop=nu1)
m.change_pop_size(0, t=t3, size_pop=nu1B)
m.change_pop_size(1, t=t2, size_pop=nu2B)
m.move_lineages(1, 0, t=t4, size_pop=N_a)
translated_model = m.translate_to(EpochDemographicModel, var2values)
em = EpochDemographicModel(gen_time=29, mutation_rate=1.25e-8)
em.add_split(0, [nu1B, nu2B])
em.add_epoch(operation_creation(Subtraction, t4, t3), [nu1B, nu2B])
em.add_epoch(operation_creation(Subtraction, t3, t2), [nu1, nu2B])
em.add_epoch(operation_creation(Subtraction, t2, t1), [nu1, nu2F])
em.add_epoch(operation_creation(Subtraction, t1, 0), [nu1F, nu2F])
self.assertEqual(2, translated_model.number_of_populations())
self.assertEqual(translated_model, em)
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, [])