def verify_dump_equality(self, ts):
"""
Verifies that we can dump a copy of the specified tree sequence
to the specified file, and load an identical copy.
"""
ts.dump(self.temp_file)
ts2 = _tskit.TreeSequence()
ts2.load(self.temp_file)
self.assertEqual(ts.get_num_samples(), ts2.get_num_samples())
self.assertEqual(ts.get_sequence_length(), ts2.get_sequence_length())
self.assertEqual(ts.get_num_mutations(), ts2.get_num_mutations())
self.assertEqual(ts.get_num_nodes(), ts2.get_num_nodes())
records1 = [ts.get_edge(j) for j in range(ts.get_num_edges())]
records2 = [ts2.get_edge(j) for j in range(ts2.get_num_edges())]
self.assertEqual(records1, records2)
mutations1 = [
ts.get_mutation(j) for j in range(ts.get_num_mutations())
]
mutations2 = [
ts2.get_mutation(j) for j in range(ts2.get_num_mutations())
]
self.assertEqual(mutations1, mutations2)
provenances1 = [
ts.get_provenance(j) for j in range(ts.get_num_provenances())
]
provenances2 = [
ts2.get_provenance(j) for j in range(ts2.get_num_provenances())
]
self.assertEqual(provenances1, provenances2)
def f(mutations):
position = []
node = []
site = []
ancestral_state = []
ancestral_state_offset = [0]
derived_state = []
derived_state_offset = [0]
for j, (p, n) in enumerate(mutations):
site.append(j)
position.append(p)
ancestral_state.append("0")
ancestral_state_offset.append(ancestral_state_offset[-1] + 1)
derived_state.append("1")
derived_state_offset.append(derived_state_offset[-1] + 1)
node.append(n)
tables.sites.set_columns(
dict(position=position,
ancestral_state=ancestral_state,
ancestral_state_offset=ancestral_state_offset,
metadata=None,
metadata_offset=None))
tables.mutations.set_columns(
dict(site=site,
node=node,
derived_state=derived_state,
derived_state_offset=derived_state_offset,
parent=None,
metadata=None,
metadata_offset=None))
ts2 = _tskit.TreeSequence()
ts2.load_tables(tables)
def test_initial_state(self):
# Check the initial state to make sure that it is empty.
ts = _tskit.TreeSequence()
self.assertRaises(ValueError, ts.get_num_samples)
self.assertRaises(ValueError, ts.get_sequence_length)
self.assertRaises(ValueError, ts.get_num_trees)
self.assertRaises(ValueError, ts.get_num_edges)
self.assertRaises(ValueError, ts.get_num_mutations)
self.assertRaises(ValueError, ts.get_num_migrations)
self.assertRaises(ValueError, ts.get_num_migrations)
self.assertRaises(ValueError, ts.get_genotype_matrix)
self.assertRaises(ValueError, ts.dump)
def test_uninitialised_tree_sequence(self):
ts = _tskit.TreeSequence()
self.assertRaises(ValueError, _tskit.LdCalculator, ts)
def test_uninitialised_tree_sequence(self):
ts = _tskit.TreeSequence()
self.assertRaises(ValueError, _tskit.HaplotypeGenerator, ts)
def test_uninitialised_tree_sequence(self):
ts = _tskit.TreeSequence()
self.assertRaises(ValueError, _tskit.VcfConverter, ts)
def loader(*args):
ts2 = _tskit.TreeSequence()
ts2.load(*args)