def test_different_lengths_error(self):
ts1 = msprime.simulate(2, length=10, random_seed=1)
ts2 = msprime.simulate(2, length=11, random_seed=1)
with pytest.raises(ValueError):
list(tsinfer.tree_pairs(ts1, ts2))
with pytest.raises(ValueError):
list(tsinfer.tree_pairs(ts2, ts1))
def test_same_ts(self):
n = 15
ts = msprime.simulate(n, recombination_rate=10, random_seed=10)
self.assertGreater(ts.num_trees, 1)
count = 0
for (left, right), tree1, tree2 in tsinfer.tree_pairs(ts, ts):
self.assertEqual((left, right), tree1.interval)
self.assertEqual(tree1.interval, tree2.interval)
self.assertEqual(tree1.parent_dict, tree2.parent_dict)
count += 1
self.assertEqual(count, ts.num_trees)
def test_same_ts(self):
n = 15
ts = msprime.simulate(n, recombination_rate=10, random_seed=10)
assert ts.num_trees > 1
count = 0
for (left, right), tree1, tree2 in tsinfer.tree_pairs(ts, ts):
assert (left, right) == tree1.interval
assert tree1.interval == tree2.interval
assert tree1.parent_dict == tree2.parent_dict
count += 1
assert count == ts.num_trees
def test_single_tree(self):
n = 10
ts1 = msprime.simulate(n, random_seed=10)
ts2 = msprime.simulate(n, random_seed=10)
self.assertEqual(ts1.num_trees, 1)
self.assertEqual(ts2.num_trees, 1)
count = 0
for (left, right), tree1, tree2 in tsinfer.tree_pairs(ts1, ts2):
self.assertEqual((0, 1), tree1.interval)
self.assertEqual((0, 1), tree2.interval)
self.assertIs(tree1.tree_sequence, ts1)
self.assertIs(tree2.tree_sequence, ts2)
count += 1
self.assertEqual(count, 1)
def test_single_tree(self):
n = 10
ts1 = msprime.simulate(n, random_seed=10)
ts2 = msprime.simulate(n, random_seed=10)
assert ts1.num_trees == 1
assert ts2.num_trees == 1
count = 0
for (_left, _right), tree1, tree2 in tsinfer.tree_pairs(ts1, ts2):
assert (0, 1) == tree1.interval
assert (0, 1) == tree2.interval
assert tree1.tree_sequence is ts1
assert tree2.tree_sequence is ts2
count += 1
assert count == 1
def test_many_trees(self):
ts1 = msprime.simulate(20, recombination_rate=20, random_seed=10)
ts2 = msprime.simulate(30, recombination_rate=10, random_seed=10)
self.assertGreater(ts1.num_trees, 1)
self.assertGreater(ts2.num_trees, 1)
breakpoints = [0]
for (left, right), tree2, tree1 in tsinfer.tree_pairs(ts2, ts1):
breakpoints.append(right)
self.assertGreaterEqual(left, tree1.interval[0])
self.assertGreaterEqual(left, tree2.interval[0])
self.assertLessEqual(right, tree1.interval[1])
self.assertLessEqual(right, tree2.interval[1])
self.assertIs(tree1.tree_sequence, ts1)
self.assertIs(tree2.tree_sequence, ts2)
all_breakpoints = set(ts1.breakpoints()) | set(ts2.breakpoints())
self.assertEqual(breakpoints, sorted(all_breakpoints))
def test_many_trees(self):
ts1 = msprime.simulate(20, recombination_rate=20, random_seed=10)
ts2 = msprime.simulate(30, recombination_rate=10, random_seed=10)
assert ts1.num_trees > 1
assert ts2.num_trees > 1
breakpoints = [0]
for (left, right), tree2, tree1 in tsinfer.tree_pairs(ts2, ts1):
breakpoints.append(right)
assert left >= tree1.interval[0]
assert left >= tree2.interval[0]
assert right <= tree1.interval[1]
assert right <= tree2.interval[1]
assert tree1.tree_sequence is ts1
assert tree2.tree_sequence is ts2
all_breakpoints = set(ts1.breakpoints()) | set(ts2.breakpoints())
assert breakpoints == sorted(all_breakpoints)
def test_many_trees_single_tree(self):
n = 10
ts1 = msprime.simulate(n, random_seed=10)
ts2 = msprime.simulate(n, recombination_rate=10, random_seed=10)
self.assertEqual(ts1.num_trees, 1)
self.assertGreater(ts2.num_trees, 1)
trees2 = ts2.trees()
count = 0
for (left, right), tree2, tree1 in tsinfer.tree_pairs(ts2, ts1):
self.assertEqual((0, 1), tree1.interval)
self.assertIs(tree1.tree_sequence, ts1)
self.assertIs(tree2.tree_sequence, ts2)
tree2p = next(trees2, None)
if tree2p is not None:
self.assertEqual(tree2.interval, tree2p.interval)
self.assertEqual(tree2.parent_dict, tree2p.parent_dict)
count += 1
self.assertEqual(count, ts2.num_trees)
def test_many_trees_single_tree(self):
n = 10
ts1 = msprime.simulate(n, random_seed=10)
ts2 = msprime.simulate(n, recombination_rate=10, random_seed=10)
assert ts1.num_trees == 1
assert ts2.num_trees > 1
trees2 = ts2.trees()
count = 0
for (_left, _right), tree2, tree1 in tsinfer.tree_pairs(ts2, ts1):
assert (0, 1) == tree1.interval
assert tree1.tree_sequence is ts1
assert tree2.tree_sequence is ts2
tree2p = next(trees2, None)
if tree2p is not None:
assert tree2.interval == tree2p.interval
assert tree2.parent_dict == tree2p.parent_dict
count += 1
assert count == ts2.num_trees
def test_different_lengths_error(self):
ts1 = msprime.simulate(2, length=10, random_seed=1)
ts2 = msprime.simulate(2, length=11, random_seed=1)
self.assertRaises(ValueError, list, tsinfer.tree_pairs(ts1, ts2))
self.assertRaises(ValueError, list, tsinfer.tree_pairs(ts2, ts1))
