def test_n_5_sites(self):
ts = tsutil.caterpillar_tree(5, num_sites=4)
self.verify(ts, 5)
self.assertEqual(ts.num_sites, 4)
self.assertEqual(ts.num_mutations, 4)
self.assertEqual(list(ts.tables.sites.position), [0.2, 0.4, 0.6, 0.8])
ts = tsutil.caterpillar_tree(5, num_sites=1, num_mutations=1)
self.assertEqual(ts.num_sites, 1)
self.assertEqual(ts.num_mutations, 1)
site = ts.site(0)
self.assertEqual(site.mutations[0].node, 7)
def test_n_5_sites(self):
ts = tsutil.caterpillar_tree(5, num_sites=4)
self.verify(ts, 5)
assert ts.num_sites == 4
assert ts.num_mutations == 4
assert list(ts.tables.sites.position) == [0.2, 0.4, 0.6, 0.8]
ts = tsutil.caterpillar_tree(5, num_sites=1, num_mutations=1)
assert ts.num_sites == 1
assert ts.num_mutations == 1
site = ts.site(0)
assert site.mutations[0].node == 7
def test_n_many_mutations(self):
for n in range(10, 15):
for num_mutations in range(0, n - 1):
ts = tsutil.caterpillar_tree(n,
num_sites=1,
num_mutations=num_mutations)
self.verify(ts, n)
self.assertEqual(ts.num_sites, 1)
self.assertEqual(ts.num_mutations, num_mutations)
for num_mutations in range(n - 1, n + 2):
with self.assertRaises(ValueError):
tsutil.caterpillar_tree(n,
num_sites=1,
num_mutations=num_mutations)
def test_n_many_mutations(self):
for n in range(10, 15):
for num_mutations in range(0, n - 1):
ts = tsutil.caterpillar_tree(n,
num_sites=1,
num_mutations=num_mutations)
self.verify(ts, n)
assert ts.num_sites == 1
assert ts.num_mutations == num_mutations
for num_mutations in range(n - 1, n + 2):
with pytest.raises(ValueError):
tsutil.caterpillar_tree(n,
num_sites=1,
num_mutations=num_mutations)
def test_n_5_mutations(self):
ts = tsutil.caterpillar_tree(5, num_sites=1, num_mutations=3)
self.verify(ts, 5)
self.assertEqual(ts.num_sites, 1)
self.assertEqual(ts.num_mutations, 3)
node = ts.tables.mutations.node
self.assertEqual(list(node), [7, 6, 5])
def test_n_5_mutations(self):
ts = tsutil.caterpillar_tree(5, num_sites=1, num_mutations=3)
self.verify(ts, 5)
assert ts.num_sites == 1
assert ts.num_mutations == 3
node = ts.tables.mutations.node
assert list(node) == [7, 6, 5]
def test_n_50(self):
ts = tsutil.caterpillar_tree(50)
self.verify(ts, 50)
def test_n_3(self):
ts = tsutil.caterpillar_tree(3)
self.verify(ts, 3)
def test_n_2(self):
ts = tsutil.caterpillar_tree(2)
self.verify(ts, 2)
