def test_options(self):
ts = self.get_example_tree_sequence()
st = _tskit.Tree(ts)
self.assertEqual(st.get_options(), 0)
# We should still be able to count the samples, just inefficiently.
self.assertEqual(st.get_num_samples(0), 1)
self.assertRaises(_tskit.LibraryError, st.get_num_tracked_samples, 0)
all_options = [
0, _tskit.SAMPLE_COUNTS, _tskit.SAMPLE_LISTS,
_tskit.SAMPLE_COUNTS | _tskit.SAMPLE_LISTS
]
for options in all_options:
tree = _tskit.Tree(ts, options=options)
copy = tree.copy()
for st in [tree, copy]:
self.assertEqual(st.get_options(), options)
self.assertEqual(st.get_num_samples(0), 1)
if options & _tskit.SAMPLE_COUNTS:
self.assertEqual(st.get_num_tracked_samples(0), 0)
else:
self.assertRaises(_tskit.LibraryError,
st.get_num_tracked_samples, 0)
if options & _tskit.SAMPLE_LISTS:
self.assertEqual(0, st.get_left_sample(0))
self.assertEqual(0, st.get_right_sample(0))
else:
self.assertRaises(ValueError, st.get_left_sample, 0)
self.assertRaises(ValueError, st.get_right_sample, 0)
self.assertRaises(ValueError, st.get_next_sample, 0)
def test_sample_list(self):
options = _tskit.SAMPLE_COUNTS | _tskit.SAMPLE_LISTS
# Note: we're assuming that samples are 0-n here.
for ts in self.get_example_tree_sequences():
t = _tskit.Tree(ts, options=options)
while t.next():
# All sample nodes should have themselves.
for j in range(ts.get_num_samples()):
self.assertEqual(t.get_left_sample(j), j)
self.assertEqual(t.get_right_sample(j), j)
# All non-tree nodes should have 0
for j in range(t.get_num_nodes()):
if t.get_parent(j) == _tskit.NULL \
and t.get_left_child(j) == _tskit.NULL:
self.assertEqual(t.get_left_sample(j), _tskit.NULL)
self.assertEqual(t.get_right_sample(j), _tskit.NULL)
# The roots should have all samples.
u = t.get_left_root()
samples = []
while u != _tskit.NULL:
sample = t.get_left_sample(u)
end = t.get_right_sample(u)
while True:
samples.append(sample)
if sample == end:
break
sample = t.get_next_sample(sample)
u = t.get_right_sib(u)
self.assertEqual(sorted(samples),
list(range(ts.get_num_samples())))
def test_index(self):
for ts in self.get_example_tree_sequences():
st = _tskit.Tree(ts)
index = 0
while st.next():
self.assertEqual(index, st.get_index())
index += 1
def test_newick_precision(self):
def get_times(tree):
"""
Returns the time strings from the specified newick tree.
"""
ret = []
current_time = None
for c in tree:
if c == ":":
current_time = ""
elif c in [",", ")"]:
ret.append(current_time)
current_time = None
elif current_time is not None:
current_time += c
return ret
ts = self.get_example_tree_sequence()
st = _tskit.Tree(ts)
while st.next():
self.assertRaises(ValueError, st.get_newick, root=0, precision=-1)
self.assertRaises(ValueError, st.get_newick, root=0, precision=17)
self.assertRaises(ValueError, st.get_newick, root=0, precision=100)
for precision in range(17):
tree = st.get_newick(root=st.get_left_root(),
precision=precision).decode()
times = get_times(tree)
self.assertGreater(len(times), ts.get_num_samples())
for t in times:
if precision == 0:
self.assertNotIn(".", t)
else:
point = t.find(".")
self.assertEqual(precision, len(t) - point - 1)
def test_sites(self):
for ts in self.get_example_tree_sequences():
st = _tskit.Tree(ts)
all_sites = [ts.get_site(j) for j in range(ts.get_num_sites())]
all_tree_sites = []
j = 0
mutation_id = 0
while st.next():
tree_sites = st.get_sites()
self.assertEqual(st.get_num_sites(), len(tree_sites))
all_tree_sites.extend(tree_sites)
for position, ancestral_state, mutations, index, metadata in tree_sites:
self.assertTrue(st.get_left() <= position < st.get_right())
self.assertEqual(index, j)
self.assertEqual(metadata, b"")
for mut_id in mutations:
site, node, derived_state, parent, metadata = \
ts.get_mutation(mut_id)
self.assertEqual(site, index)
self.assertEqual(mutation_id, mut_id)
self.assertNotEqual(st.get_parent(node), _tskit.NULL)
self.assertEqual(metadata, b"")
mutation_id += 1
j += 1
self.assertEqual(all_tree_sites, all_sites)
def test_copy(self):
for ts in self.get_example_tree_sequences():
t1 = _tskit.Tree(ts)
t2 = t1.copy()
self.assertEqual(t1.get_index(), t2.get_index())
self.assertIsNot(t1, t2)
while t1.next():
t2 = t1.copy()
self.assertEqual(t1.get_index(), t2.get_index())
def test_mrca_interface(self):
for ts in self.get_example_tree_sequences():
num_nodes = ts.get_num_nodes()
st = _tskit.Tree(ts)
for v in [num_nodes, 10**6, _tskit.NULL]:
self.assertRaises(ValueError, st.get_mrca, v, v)
self.assertRaises(ValueError, st.get_mrca, v, 1)
self.assertRaises(ValueError, st.get_mrca, 1, v)
# All the mrcas for an uninitialised tree should be _tskit.NULL
for u, v in itertools.combinations(range(num_nodes), 2):
self.assertEqual(st.get_mrca(u, v), _tskit.NULL)
def test_equality(self):
last_ts = None
for ts in self.get_example_tree_sequences():
t1 = _tskit.Tree(ts)
t2 = _tskit.Tree(ts)
self.assertTrue(t1.equals(t2))
self.assertTrue(t2.equals(t1))
while True:
self.assertTrue(t1.equals(t2))
self.assertTrue(t2.equals(t1))
n1 = t1.next()
self.assertFalse(t1.equals(t2))
self.assertFalse(t2.equals(t1))
n2 = t2.next()
self.assertEqual(n1, n2)
if not n1:
break
if last_ts is not None:
t2 = _tskit.Tree(last_ts)
self.assertFalse(t1.equals(t2))
self.assertFalse(t2.equals(t1))
last_ts = ts
def test_newick_interface(self):
ts = self.get_example_tree_sequence()
st = _tskit.Tree(ts)
# TODO this will break when we correctly handle multiple roots.
self.assertEqual(st.get_newick(0), b"1;")
for bad_type in [None, "", [], {}]:
self.assertRaises(TypeError, st.get_newick, precision=bad_type)
self.assertRaises(TypeError,
st.get_newick,
ts,
time_scale=bad_type)
while st.next():
newick = st.get_newick(st.get_left_root())
self.assertTrue(newick.endswith(b";"))
def test_count_tracked_samples(self):
# Ensure that there are some non-binary nodes.
non_binary = False
for ts in self.get_example_tree_sequences():
st = _tskit.Tree(ts)
while st.next():
for u in range(ts.get_num_nodes()):
if len(st.get_children(u)) > 1:
non_binary = True
samples = [j for j in range(ts.get_num_samples())]
powerset = itertools.chain.from_iterable(
itertools.combinations(samples, r)
for r in range(len(samples) + 1))
max_sets = 100
for _, subset in zip(range(max_sets), map(list, powerset)):
# Ordering shouldn't make any difference.
random.shuffle(subset)
st = _tskit.Tree(ts,
options=_tskit.SAMPLE_COUNTS,
tracked_samples=subset)
while st.next():
nu = get_tracked_sample_counts(st, subset)
nu_prime = [
st.get_num_tracked_samples(j)
for j in range(st.get_num_nodes())
]
self.assertEqual(nu, nu_prime)
# Passing duplicated values should raise an error
sample = 1
for j in range(2, 20):
tracked_samples = [sample for _ in range(j)]
self.assertRaises(_tskit.LibraryError,
_tskit.Tree,
ts,
options=_tskit.SAMPLE_COUNTS,
tracked_samples=tracked_samples)
self.assertTrue(non_binary)
def test_bounds_checking(self):
for ts in self.get_example_tree_sequences():
n = ts.get_num_nodes()
st = _tskit.Tree(ts,
options=_tskit.SAMPLE_COUNTS
| _tskit.SAMPLE_LISTS)
for v in [-100, -1, n + 1, n + 100, n * 100]:
self.assertRaises(ValueError, st.get_parent, v)
self.assertRaises(ValueError, st.get_children, v)
self.assertRaises(ValueError, st.get_time, v)
self.assertRaises(ValueError, st.get_left_sample, v)
self.assertRaises(ValueError, st.get_right_sample, v)
self.assertRaises(ValueError, st.is_descendant, v, 0)
self.assertRaises(ValueError, st.is_descendant, 0, v)
n = ts.get_num_samples()
for v in [-100, -1, n + 1, n + 100, n * 100]:
self.assertRaises(ValueError, st.get_next_sample, v)
def test_cleared_tree(self):
ts = self.get_example_tree_sequence()
samples = ts.get_samples()
def check_tree(tree):
self.assertEqual(tree.get_index(), -1)
self.assertEqual(tree.get_left_root(), samples[0])
self.assertEqual(tree.get_mrca(0, 1), _tskit.NULL)
for u in range(ts.get_num_nodes()):
self.assertEqual(tree.get_parent(u), _tskit.NULL)
self.assertEqual(tree.get_left_child(u), _tskit.NULL)
self.assertEqual(tree.get_right_child(u), _tskit.NULL)
tree = _tskit.Tree(ts)
check_tree(tree)
while tree.next():
pass
check_tree(tree)
while tree.prev():
pass
check_tree(tree)
def test_while_loop_semantics(self):
for ts in self.get_example_tree_sequences():
tree = _tskit.Tree(ts)
# Any mixture of prev and next is OK and gives a valid iteration.
for _ in range(2):
j = 0
while tree.next():
self.assertEqual(tree.get_index(), j)
j += 1
self.assertEqual(j, ts.get_num_trees())
for _ in range(2):
j = ts.get_num_trees()
while tree.prev():
self.assertEqual(tree.get_index(), j - 1)
j -= 1
self.assertEqual(j, 0)
j = 0
while tree.next():
self.assertEqual(tree.get_index(), j)
j += 1
self.assertEqual(j, ts.get_num_trees())
def test_count_all_samples(self):
for ts in self.get_example_tree_sequences():
self.verify_iterator(_tskit.TreeDiffIterator(ts))
st = _tskit.Tree(ts, options=_tskit.SAMPLE_COUNTS)
# Without initialisation we should be 0 samples for every node
# that is not a sample.
for j in range(st.get_num_nodes()):
count = 1 if j < ts.get_num_samples() else 0
self.assertEqual(st.get_num_samples(j), count)
self.assertEqual(st.get_num_tracked_samples(j), 0)
while st.next():
nu = get_sample_counts(ts, st)
nu_prime = [
st.get_num_samples(j) for j in range(st.get_num_nodes())
]
self.assertEqual(nu, nu_prime)
# For tracked samples, this should be all zeros.
nu = [
st.get_num_tracked_samples(j)
for j in range(st.get_num_nodes())
]
self.assertEqual(nu, list([0 for _ in nu]))
def test_constructor(self):
self.assertRaises(TypeError, _tskit.Tree)
for bad_type in ["", {}, [], None, 0]:
self.assertRaises(TypeError, _tskit.Tree, bad_type)
ts = self.get_example_tree_sequence()
for bad_type in ["", {}, True, 1, None]:
self.assertRaises(TypeError,
_tskit.Tree,
ts,
tracked_samples=bad_type)
for bad_type in ["", {}, None, []]:
self.assertRaises(TypeError, _tskit.Tree, ts, options=bad_type)
for ts in self.get_example_tree_sequences():
st = _tskit.Tree(ts)
self.assertEqual(st.get_num_nodes(), ts.get_num_nodes())
# An uninitialised sparse tree should always be zero.
self.assertEqual(st.get_left_root(), 0)
self.assertEqual(st.get_left(), 0)
self.assertEqual(st.get_right(), 0)
for j in range(ts.get_num_samples()):
self.assertEqual(st.get_parent(j), _tskit.NULL)
self.assertEqual(st.get_children(j), tuple())
self.assertEqual(st.get_time(j), 0)