def test_decode_errors(self):
with self.assertRaises(ValueError):
pyslim.decode_mutation(2.0)
with self.assertRaises(ValueError):
pyslim.decode_mutation([2.0, 3.0])
with self.assertRaises(ValueError):
pyslim.decode_node(2.0)
with self.assertRaises(ValueError):
pyslim.decode_node([1, 2])
with self.assertRaises(ValueError):
pyslim.decode_individual(3.0)
with self.assertRaises(ValueError):
pyslim.decode_individual([1, 2])
with self.assertRaises(ValueError):
pyslim.decode_population(1.0)
with self.assertRaises(ValueError):
pyslim.decode_population([2, 3])
def test_individual_metadata(self):
md = pyslim.IndividualMetadata(
age=2, pedigree_id=23, population=0,
sex=pyslim.INDIVIDUAL_TYPE_MALE,
flags=pyslim.INDIVIDUAL_FLAG_MIGRATED)
md_bytes = pyslim.encode_individual(md)
new_md = pyslim.decode_individual(md_bytes)
self.assertEqual(md, new_md)
def test_decode_already_individual(self):
m = pyslim.IndividualMetadata(pedigree_id=24,
age=8,
population=1,
sex=1,
flags=0)
dm = pyslim.decode_individual(m)
self.assertEqual(m, dm)
def test_legacy_errors(self):
defaults = pyslim.default_slim_metadata
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_mutation(defaults('mutation'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_population(defaults('population'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_individual(defaults('individual'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.decode_node(defaults('node'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_mutation(defaults('mutation'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_population(defaults('population'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_individual(defaults('individual'))
with self.assertRaisesRegex(ValueError, "legacy"):
pyslim.encode_node(defaults('node'))
def test_individual_derived_info(self):
for ts in self.get_slim_examples():
for j, ind in enumerate(ts.individuals()):
a = ts.tables.individuals.metadata_offset[j]
b = ts.tables.individuals.metadata_offset[j+1]
raw_md = ts.tables.individuals.metadata[a:b]
md = pyslim.decode_individual(raw_md)
self.assertEqual(ind.metadata, md)
self.assertEqual(ts.individual(j).metadata, md)
for n in ind.nodes:
self.assertEqual(ts.node(n).population, ind.population)
self.assertEqual(ts.node(n).time, ind.time)
def test_annotate_individuals(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.individuals.metadata,
tables.individuals.metadata_offset):
dm = pyslim.decode_individual(md)
edm = pyslim.encode_individual(dm)
self.assertEqual(md, edm)
metadata.append(dm)
pyslim.annotate_individual_metadata(new_tables, metadata)
self.assertEqual(tables, new_tables)
def test_annotate_individuals(self):
for ts in get_msprime_examples():
slim_ts = pyslim.annotate_defaults(ts, model_type="nonWF", slim_generation=1)
tables = slim_ts.tables
metadata = list(pyslim.extract_individual_metadata(tables))
self.assertEqual(len(metadata), slim_ts.num_individuals)
sexes = [random.choice([pyslim.INDIVIDUAL_TYPE_FEMALE, pyslim.INDIVIDUAL_TYPE_MALE])
for _ in metadata]
for j in range(len(metadata)):
metadata[j].sex = sexes[j]
pyslim.annotate_individual_metadata(tables, metadata)
new_ts = pyslim.load_tables(tables)
for j, ind in enumerate(new_ts.individuals()):
md = pyslim.decode_individual(ind.metadata)
self.assertEqual(md.sex, sexes[j])
def test_annotate_individuals(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.individuals.metadata,
tables.individuals.metadata_offset):
with self.assertWarns(DeprecationWarning):
dm = pyslim.decode_individual(md)
with self.assertWarns(DeprecationWarning):
edm = pyslim.encode_individual(dm)
self.assertEqual(md, edm)
metadata.append(dm)
with self.assertWarns(DeprecationWarning):
pyslim.annotate_individual_metadata(new_tables, metadata)
self.assertTableCollectionsEqual(tables, new_tables)
def individual_populations(self, inds=None):
if inds is None:
inds = self.individuals()
return np.fromiter(map(lambda x: pyslim.decode_individual(x.metadata).population, inds), 'int')
node_metadata = []
for md in msprime.unpack_bytes(tables.nodes.metadata,
tables.nodes.metadata_offset):
dn = pyslim.decode_node(md)
edn = pyslim.encode_node(dn)
assert (md == edn)
node_metadata.append(dn)
pyslim.annotate_nodes(tables, node_metadata)
# individuals
individual_metadata = []
for md in msprime.unpack_bytes(tables.individuals.metadata,
tables.individuals.metadata_offset):
di = pyslim.decode_individual(md)
edi = pyslim.encode_individual(di)
assert (md == edi)
individual_metadata.append(di)
pyslim.annotate_individuals(tables, individual_metadata)
# populations
population_metadata = []
for md in msprime.unpack_bytes(tables.populations.metadata,
tables.populations.metadata_offset):
if len(md) > 0:
dp = pyslim.decode_population(md)
edp = pyslim.encode_population(dp)
assert (md == edp)
