def test_node_metadata(self):
md = pyslim.NodeMetadata(slim_id=2,
is_null=False,
genome_type=pyslim.GENOME_TYPE_X)
md_bytes = pyslim.encode_node(md)
new_md = pyslim.decode_node(md_bytes)
self.assertEqual(md, new_md)
def get_slim_ids(self, ts):
# get SLiM ID -> msprime ID map from metadata
ids = {}
for n in ts.nodes():
meta = pyslim.decode_node(n.metadata)
ids[meta.slim_id] = n.id
return ids
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_node_metadata(self):
md = pyslim.NodeMetadata(slim_id=2,
is_null=False,
genome_type=pyslim.GENOME_TYPE_X)
with self.assertWarns(DeprecationWarning):
md_bytes = pyslim.encode_node(md)
with self.assertWarns(DeprecationWarning):
new_md = pyslim.decode_node(md_bytes)
self.assertEqual(md, new_md)
def test_node_derived_info(self):
for ts in self.get_slim_examples():
for j, node in enumerate(ts.nodes()):
a = ts.tables.nodes.metadata_offset[j]
b = ts.tables.nodes.metadata_offset[j+1]
raw_md = ts.tables.nodes.metadata[a:b]
md = pyslim.decode_node(raw_md)
self.assertEqual(node.metadata, md)
self.assertEqual(ts.node(j).metadata, md)
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_annotate_nodes(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.nodes.metadata,
tables.nodes.metadata_offset):
dm = pyslim.decode_node(md)
edm = pyslim.encode_node(dm)
self.assertEqual(md, edm)
metadata.append(dm)
pyslim.annotate_node_metadata(new_tables, metadata)
self.assertEqual(tables, new_tables)
def test_annotate_nodes(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.nodes.metadata,
tables.nodes.metadata_offset):
with self.assertWarns(DeprecationWarning):
dm = pyslim.decode_node(md)
with self.assertWarns(DeprecationWarning):
edm = pyslim.encode_node(dm)
self.assertEqual(md, edm)
metadata.append(dm)
with self.assertWarns(DeprecationWarning):
pyslim.annotate_node_metadata(new_tables, metadata)
self.assertTableCollectionsEqual(tables, new_tables)
def test_annotate_nodes(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_node_metadata(tables))
self.assertEqual(len(metadata), slim_ts.num_nodes)
gtypes = [random.choice([pyslim.GENOME_TYPE_X, pyslim.GENOME_TYPE_Y])
for _ in metadata]
for j in range(len(metadata)):
if metadata[j] is not None:
metadata[j].genome_type = gtypes[j]
pyslim.annotate_node_metadata(tables, metadata)
new_ts = pyslim.load_tables(tables)
for j, x in enumerate(new_ts.nodes()):
md = pyslim.decode_node(x.metadata)
if md is not None:
self.assertEqual(md.genome_type, gtypes[j])
def test_decode_already_node(self):
m = pyslim.NodeMetadata(slim_id=123, is_null=True, genome_type=0)
with self.assertWarns(DeprecationWarning):
dm = pyslim.decode_node(m)
self.assertEqual(m, dm)
mut_metadata = []
for md in msprime.unpack_bytes(tables.mutations.metadata,
tables.mutations.metadata_offset):
dm = pyslim.decode_mutation(md)
edm = pyslim.encode_mutation(dm)
assert (md == edm)
mut_metadata.append(dm)
pyslim.annotate_mutations(tables, mut_metadata)
# nodes
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)
def test_decode_already_node(self):
m = pyslim.NodeMetadata(slim_id=123, is_null=True, genome_type=0)
dm = pyslim.decode_node(m)
self.assertEqual(m, dm)
