def test_bad_edges(self):
msout = """
[1](1:0.27413282187548,2:0.27413282187548);
[0](1:0.27413282187548,2:0.27413282187548);
"""
with pytest.raises(tskit.TskitException):
tsconvert.from_ms(msout)
def test_equal_internal_node_time(self):
# 6
# ┏━┻━┓
# 4 5
# ┏┻┓ ┏┻┓
# 0 1 2 3
tables = tskit.TableCollection(1)
for _ in range(4):
tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE, time=0)
tables.nodes.add_row(0, time=1)
tables.nodes.add_row(0, time=1)
tables.nodes.add_row(0, time=2)
tables.edges.add_row(0, 1, 4, 0)
tables.edges.add_row(0, 1, 4, 1)
tables.edges.add_row(0, 1, 5, 2)
tables.edges.add_row(0, 1, 5, 3)
tables.edges.add_row(0, 1, 6, 4)
tables.edges.add_row(0, 1, 6, 5)
tables.sort()
ts = tables.tree_sequence()
msout = tsconvert.to_ms(ts)
# The current algorithm assumes node times are unique
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
def test_n4_example(self):
# $ mspms 4 1 -T -r 4 10 -p 8
msout = """
/home/jk/.local/bin/mspms 4 1 -T -r 4 10 -p 8
961626313 1881970557 110898863
//
[5](1:0.70961771,(4:0.33536000,(2:0.12737966,3:0.12737966):0.20798034):0.37425772);
[1]((2:0.12737966,3:0.12737966):0.20798034,(1:0.21249950,4:0.21249950):0.12286050);
[2]((3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):0.20798034,1:0.33536000);
[1](1:1.32624987,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.19887022);
[2](1:1.80041212,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.67303246);
"""
ts = tsconvert.from_ms(msout)
self.assertEqual(ts.num_samples, 4)
self.assertEqual(ts.sequence_length, 11)
self.assertEqual(ts.num_trees, 5)
trees = ts.trees()
tree = next(trees)
self.assertEqual(tree.interval, (0, 5))
self.assertAlmostEqual(tree.branch_length(0), 0.70961771)
self.assertAlmostEqual(tree.branch_length(1), 0.12737966)
self.assertAlmostEqual(tree.branch_length(2), 0.12737966)
self.assertAlmostEqual(tree.branch_length(3), 0.33536000)
tree = next(trees)
self.assertEqual(tree.interval, (5, 6))
self.assertAlmostEqual(tree.branch_length(0), 0.21249950)
self.assertAlmostEqual(tree.branch_length(1), 0.12737966)
self.assertAlmostEqual(tree.branch_length(2), 0.12737966)
self.assertAlmostEqual(tree.branch_length(3), 0.21249950)
tree = next(trees)
self.assertEqual(tree.interval, (6, 8))
tree = next(trees)
self.assertEqual(tree.interval, (8, 9))
tree = next(trees)
self.assertEqual(tree.interval, (9, 11))
self.assertAlmostEqual(tree.branch_length(0), 1.80041212)
self.assertAlmostEqual(tree.branch_length(1), 0.02380236)
self.assertAlmostEqual(tree.branch_length(2), 0.12737966)
self.assertAlmostEqual(tree.branch_length(3), 0.02380236)
# Should get the same output if we strip off the header stuff.
msout = """
[5](1:0.70961771,(4:0.33536000,(2:0.12737966,3:0.12737966):0.20798034):0.37425772);
[1]((2:0.12737966,3:0.12737966):0.20798034,(1:0.21249950,4:0.21249950):0.12286050);
[2]((3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):0.20798034,1:0.33536000);
[1](1:1.32624987,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.19887022);
[2](1:1.80041212,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.67303246);
"""
tables = tsconvert.from_ms(msout).tables
self.assertEqual(tables, ts.tables)
def test_n4_example(self):
# $ mspms 4 1 -T -r 4 10 -p 8
msout = """
/home/jk/.local/bin/mspms 4 1 -T -r 4 10 -p 8
961626313 1881970557 110898863
//
[5](1:0.70961771,(4:0.33536000,(2:0.12737966,3:0.12737966):0.20798034):0.37425772);
[1]((2:0.12737966,3:0.12737966):0.20798034,(1:0.21249950,4:0.21249950):0.12286050);
[2]((3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):0.20798034,1:0.33536000);
[1](1:1.32624987,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.19887022);
[2](1:1.80041212,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.67303246);
""" # noqa: B950 W293
ts = tsconvert.from_ms(msout)
assert ts.num_samples == 4
assert ts.sequence_length == 11
assert ts.num_trees == 5
trees = ts.trees()
tree = next(trees)
assert tree.interval == (0, 5)
assert tree.branch_length(0) == pytest.approx(0.70961771)
assert tree.branch_length(1) == pytest.approx(0.12737966)
assert tree.branch_length(2) == pytest.approx(0.12737966)
assert tree.branch_length(3) == pytest.approx(0.33536000)
tree = next(trees)
assert tree.interval == (5, 6)
assert tree.branch_length(0) == pytest.approx(0.21249950)
assert tree.branch_length(1) == pytest.approx(0.12737966)
assert tree.branch_length(2) == pytest.approx(0.12737966)
assert tree.branch_length(3) == pytest.approx(0.21249950)
tree = next(trees)
assert tree.interval == (6, 8)
tree = next(trees)
assert tree.interval == (8, 9)
tree = next(trees)
assert tree.interval == (9, 11)
assert tree.branch_length(0) == pytest.approx(1.80041212)
assert tree.branch_length(1) == pytest.approx(0.02380236)
assert tree.branch_length(2) == pytest.approx(0.12737966)
assert tree.branch_length(3) == pytest.approx(0.02380236)
# Should get the same output if we strip off the header stuff.
msout = """
[5](1:0.70961771,(4:0.33536000,(2:0.12737966,3:0.12737966):0.20798034):0.37425772);
[1]((2:0.12737966,3:0.12737966):0.20798034,(1:0.21249950,4:0.21249950):0.12286050);
[2]((3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):0.20798034,1:0.33536000);
[1](1:1.32624987,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.19887022);
[2](1:1.80041212,(3:0.12737966,(2:0.02380236,4:0.02380236):0.10357730):1.67303246);
""" # noqa: B950
tables = tsconvert.from_ms(msout).tables
tables.assert_equals(ts.tables, ignore_timestamps=True)
def test_ms_without_recombination(self):
msout = """
ms 4 1 -t 5 -T -seeds 1 2 3
1 2 3
//
((2:0.0680,3:0.0680):0.1481,(1:0.2124,4:0.2124):0.0038);
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
def test_empty_trees(self):
msout = """
[];
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
msout = """
[1];
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
def test_ms_without_trees_flag(self):
msout = """ms 3 1 -t 4 -r 5 6 -seeds 1 2 3
1 2 3
//
segsites: 3
positions: 0.3054 0.3812 0.5338
111
000
100
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
def test_nonmatching_tips(self):
msout = """
[2](1:0.2144,3:0.2144);
[4](3:0.2144,(1:0.0768,2:0.0768):0.1376);
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
msout = """
[2](2:0.2930,(1:0.2144,4:0.2144):0.0786);
[4](3:0.2144,(1:0.0768,2:0.0768):0.1376);
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
def verify(self, ts):
msout = tsconvert.to_ms(ts.simplify())
new_ts = tsconvert.from_ms(msout)
self.assertEqual(ts.num_trees, new_ts.num_trees)
for t1, t2 in zip(ts.trees(), new_ts.trees()):
self.assertAlmostEqual(t1.interval[0], t2.interval[0])
self.assertAlmostEqual(t1.interval[1], t2.interval[1])
self.assertEqual(kc_distance(t1, t2), 0)
def verify(self, ts):
msout = tsconvert.to_ms(ts.simplify())
new_ts = tsconvert.from_ms(msout)
assert ts.num_trees == new_ts.num_trees
for t1, t2 in zip(ts.trees(), new_ts.trees()):
assert t1.interval[0] == pytest.approx(t2.interval[0])
assert t1.interval[1] == pytest.approx(t2.interval[1])
assert kc_distance(t1, t2) == 0
def test_malformed_length(self):
msout = """
5(1:0.27413282187548,2:0.27413282187548);
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
msout = """
[XXX](1:0.27413282187548,2:0.27413282187548);
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
msout = """
[](1:0.27413282187548,2:0.27413282187548);
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
msout = """
[5(1:0.27413282187548,2:0.27413282187548);
"""
with pytest.raises(dendropy.utility.error.DataParseError):
tsconvert.from_ms(msout)
def test_n2_example(self):
# j$ mspms 2 1 -T -r 4 10 -p 14
msout = """
/home/jk/.local/bin/mspms 2 1 -T -r 4 10 -p 14
1774173160 1383299789 1436475231
//
[5](1:0.27413282187548,2:0.27413282187548);
[3](1:0.43103605328988,2:0.43103605328988);
[1](1:1.96842212024363,2:1.96842212024363);
[1](1:2.06027985820196,2:2.06027985820196);
"""
ts = tsconvert.from_ms(msout)
assert ts.num_samples == 2
assert ts.sequence_length == 10
assert ts.num_trees == 4
trees = ts.trees()
tree = next(trees)
assert tree.interval == (0, 5)
assert tree.branch_length(0) == pytest.approx(0.27413282187548)
assert tree.branch_length(1) == pytest.approx(0.27413282187548)
tree = next(trees)
assert tree.interval == (5, 8)
assert tree.branch_length(0) == pytest.approx(0.43103605328988)
assert tree.branch_length(1) == pytest.approx(0.43103605328988)
tree = next(trees)
assert tree.interval == (8, 9)
assert tree.branch_length(0) == pytest.approx(1.96842212024363)
assert tree.branch_length(1) == pytest.approx(1.96842212024363)
tree = next(trees)
assert tree.interval == (9, 10)
assert tree.branch_length(0) == pytest.approx(2.06027985820196)
assert tree.branch_length(1) == pytest.approx(2.06027985820196)
def test_n2_example(self):
# j$ mspms 2 1 -T -r 4 10 -p 14
msout = """
/home/jk/.local/bin/mspms 2 1 -T -r 4 10 -p 14
1774173160 1383299789 1436475231
//
[5](1:0.27413282187548,2:0.27413282187548);
[3](1:0.43103605328988,2:0.43103605328988);
[1](1:1.96842212024363,2:1.96842212024363);
[1](1:2.06027985820196,2:2.06027985820196);
"""
ts = tsconvert.from_ms(msout)
self.assertEqual(ts.num_samples, 2)
self.assertEqual(ts.sequence_length, 10)
self.assertEqual(ts.num_trees, 4)
trees = ts.trees()
tree = next(trees)
self.assertEqual(tree.interval, (0, 5))
self.assertAlmostEqual(tree.branch_length(0), 0.27413282187548)
self.assertAlmostEqual(tree.branch_length(1), 0.27413282187548)
tree = next(trees)
self.assertEqual(tree.interval, (5, 8))
self.assertAlmostEqual(tree.branch_length(0), 0.43103605328988)
self.assertAlmostEqual(tree.branch_length(1), 0.43103605328988)
tree = next(trees)
self.assertEqual(tree.interval, (8, 9))
self.assertAlmostEqual(tree.branch_length(0), 1.96842212024363)
self.assertAlmostEqual(tree.branch_length(1), 1.96842212024363)
tree = next(trees)
self.assertEqual(tree.interval, (9, 10))
self.assertAlmostEqual(tree.branch_length(0), 2.06027985820196)
self.assertAlmostEqual(tree.branch_length(1), 2.06027985820196)
def test_full_ms_output(self):
msout = """
ms 3 1 -t 4 -r 5 6 -seeds 1 2 3 -T
1 2 3
//
[2](2:0.2930,(1:0.2144,3:0.2144):0.0786);
[4](3:0.2144,(1:0.0768,2:0.0768):0.1376);
segsites: 3
positions: 0.3054 0.3812 0.5338
111
000
100
"""
ts = tsconvert.from_ms(msout)
assert ts.num_samples == 3
assert ts.sequence_length == 6
assert ts.num_trees == 2
assert ts.num_nodes == 6
trees = ts.trees()
tree = next(trees)
assert tree.interval == (0, 2)
internal_nodes = set(tree.nodes()) - set(ts.samples())
assert tree.branch_length(0) == pytest.approx(0.2144)
assert tree.branch_length(1) == pytest.approx(0.2930)
assert tree.branch_length(2) == pytest.approx(0.2144)
assert tree.branch_length(min(internal_nodes)) == pytest.approx(0.0786)
tree = next(trees)
assert tree.interval == (2, 6)
internal_nodes = set(tree.nodes()) - set(ts.samples())
assert tree.branch_length(0) == pytest.approx(0.0768)
assert tree.branch_length(1) == pytest.approx(0.0768)
assert tree.branch_length(2) == pytest.approx(0.2144)
assert tree.branch_length(min(internal_nodes)) == pytest.approx(0.1376)
def test_single_tree(self):
msout = """
[1](1:0.27413282187548,2:0.27413282187548);
"""
ts = tsconvert.from_ms(msout)
assert ts.num_trees == 1
def test_empty_input(self):
with pytest.raises(ValueError):
tsconvert.from_ms("")
def test_zero_sequence_length(self):
msout = """
[0](1:0.27413282187548,2:0.27413282187548);
"""
with pytest.raises(tskit.TskitException):
tsconvert.from_ms(msout)
def test_identical_node_times(self):
msout = """
[2](((1:1.5,2:1.5):1.7,3:3.2):1.1,(4:1.5,5:1.5):2.8);
"""
with pytest.raises(ValueError):
tsconvert.from_ms(msout)
