def verify(self, ts, samples, populations):
tab = slime.get_ancestry_table(ts,
populations=populations,
samples=samples)
# Loop through the rows of the ancestral branch table.
for row in range(0, tab.num_rows):
current_sample = tab.child[row]
current_left = tab.left[row]
current_right = tab.right[row]
current_pop = ts.tables.nodes.population[current_sample]
if current_pop in populations:
self.assertEqual(tab.population[row], current_pop)
else:
for tree in ts.trees():
if tree.interval[0] >= current_right:
break
while tree.interval[1] <= current_left:
tree.next()
# Check that that most recent node from a relevant population has the
# same population ID as listed in the ancestor table.
par = tree.get_parent(current_sample)
ancestor_pop = ts.tables.nodes.population[par]
while ancestor_pop not in populations:
par = tree.get_parent(par)
ancestor_pop = ts.tables.nodes.population[par]
self.assertEqual(tab.population[row], ancestor_pop)
def test_some_samples_have_relevant_population_labels(self):
# Tree sequence | Population
# 4 | 2
# / \ |
# / 3 | 1
# / / \ |
# 0 1 2 | 0, 1, 2
nodes = io.StringIO("""\
id is_sample population time
0 1 0 0.00000000000000
1 1 1 0.00000000000000
2 1 2 0.00000000000000
3 0 1 1.00000000000000
4 0 2 2.00000000000000
""")
edges = io.StringIO("""\
id left right parent child
0 0.00000000 1.00000000 3 1,2
1 0.00000000 1.00000000 4 0,3
""")
ts = tskit.load_text(nodes=nodes, edges=edges, strict=False)
tab = slime.get_ancestry_table(ts, populations=[1, 2])
self.assertEqual(list(tab.left), [0, 0, 0])
self.assertEqual(list(tab.right), [1, 1, 1])
self.assertEqual(list(tab.population), [2, 1, 2])
self.assertEqual(list(tab.child), [0, 1, 2])
def test_multiple_trees_some_missing_segments(self):
ts = tskit.load_text(nodes=self.nodes1,
edges=self.edges1,
strict=False)
tab = slime.get_ancestry_table(ts, [1, 2])
self.assertEqual(list(tab.left), [0, .5, 0, .5, .5, .5, 0])
self.assertEqual(list(tab.right), [.5, 1, .5, 1, 1, 1, .5])
self.assertEqual(list(tab.population), [1, 2, 1, 2, 2, 2, 1])
self.assertEqual(list(tab.child), [0, 0, 1, 1, 2, 3, 4])
def test_multiple_trees_edges_are_squashed(self):
ts = tskit.load_text(nodes=self.nodes1,
edges=self.edges1,
strict=False)
tab = slime.get_ancestry_table(ts, [3])
self.assertEqual(list(tab.left), [0, 0, 0, 0, 0])
self.assertEqual(list(tab.right), [1, 1, 1, 1, 1])
self.assertEqual(list(tab.population), [3, 3, 3, 3, 3])
self.assertEqual(list(tab.child), [0, 1, 2, 3, 4])
def test_one_population(self):
ts = tskit.load_text(nodes=self.nodes0,
edges=self.edges0,
strict=False)
tab = slime.get_ancestry_table(ts, [1, 3])
self.assertEqual(list(tab.left), [0, 0])
self.assertEqual(list(tab.right), [1, 1])
self.assertEqual(list(tab.population), [1, 1])
self.assertEqual(list(tab.child), [1, 2])
def test_no_ancestors(self):
ts = tskit.load_text(nodes=self.nodes0,
edges=self.edges0,
strict=False)
with self.assertRaises(ValueError):
slime.get_ancestry_table(ts, samples=[0], populations=[3])
def test_no_rows(self):
ts = tskit.load_text(nodes=self.nodes0,
edges=self.edges0,
strict=False)
tab = slime.get_ancestry_table(ts, samples=[0], populations=[1])
self.assertEqual(tab.num_rows, 0)
def test_simple_case(self):
tab = slime.get_ancestry_table(self.ts_ex, list(self.populations_ex))