def test_json(self):
ts = msprime.simulate(10, random_seed=1)
tables = ts.dump_tables()
nodes = tables.nodes
# For each node, we create some Python metadata that can be JSON encoded.
metadata = [{
"one": j,
"two": 2 * j,
"three": list(range(j))
} for j in range(len(nodes))]
encoded, offset = msprime.pack_strings(map(json.dumps, metadata))
nodes.set_columns(flags=nodes.flags,
time=nodes.time,
population=nodes.population,
metadata_offset=offset,
metadata=encoded)
self.assertTrue(np.array_equal(nodes.metadata_offset, offset))
self.assertTrue(np.array_equal(nodes.metadata, encoded))
ts1 = msprime.load_tables(nodes=nodes, edges=tables.edges)
for j, node in enumerate(ts1.nodes()):
decoded_metadata = json.loads(node.metadata.decode())
self.assertEqual(decoded_metadata, metadata[j])
ts1.dump(self.temp_file)
ts2 = msprime.load(self.temp_file)
self.assertEqual(ts1.tables.nodes, ts2.tables.nodes)
def test_simple_case(self):
strings = ["hello", "world"]
packed, length = msprime.pack_strings(strings)
self.assertEqual(list(length), [5, 5])
self.assertEqual(packed.shape, (10, ))
returned = msprime.unpack_strings(packed, length)
self.assertEqual(returned, strings)
def verify_packing(self, strings):
packed, length = msprime.pack_strings(strings)
self.assertEqual(packed.dtype, np.int8)
self.assertEqual(length.dtype, np.uint32)
self.assertEqual(list(length), [len(s) for s in strings])
self.assertEqual(packed.shape[0], np.sum(length))
returned = msprime.unpack_strings(packed, length)
self.assertEqual(strings, returned)
def node_metadata_example():
ts = msprime.simulate(
sample_size=100, recombination_rate=0.1, length=10, random_seed=1)
nodes = msprime.NodeTable()
edges = msprime.EdgeTable()
ts.dump_tables(nodes=nodes, edges=edges)
new_nodes = msprime.NodeTable()
metadatas = ["n_{}".format(u) for u in range(ts.num_nodes)]
packed, offset = msprime.pack_strings(metadatas)
new_nodes.set_columns(
metadata=packed, metadata_offset=offset, flags=nodes.flags, time=nodes.time)
return msprime.load_tables(nodes=new_nodes, edges=edges)
def test_optional_population(self):
for num_rows in [0, 10, 100]:
names = [str(j) for j in range(num_rows)]
name, name_length = msprime.pack_strings(names)
flags = list(range(num_rows))
time = list(range(num_rows))
table = msprime.NodeTable()
table.set_columns(name=name,
name_length=name_length,
flags=flags,
time=time)
self.assertEqual(list(table.population),
[-1 for _ in range(num_rows)])
self.assertEqual(list(table.flags), flags)
self.assertEqual(list(table.time), time)
self.assertEqual(list(table.name), list(name))
self.assertEqual(list(table.name_length), list(name_length))
def test_random_names(self):
for num_rows in [0, 10, 100]:
names = [random_string(10) for _ in range(num_rows)]
name, name_length = msprime.pack_strings(names)
flags = list(range(num_rows))
time = list(range(num_rows))
table = msprime.NodeTable()
table.set_columns(name=name,
name_length=name_length,
flags=flags,
time=time)
self.assertEqual(list(table.flags), flags)
self.assertEqual(list(table.time), time)
self.assertEqual(list(table.name), list(name))
self.assertEqual(list(table.name_length), list(name_length))
unpacked_names = msprime.unpack_strings(table.name,
table.name_length)
self.assertEqual(names, unpacked_names)
def node_name_example():
ts = msprime.simulate(sample_size=100,
recombination_rate=0.1,
length=10,
random_seed=1)
nodes = msprime.NodeTable()
edgesets = msprime.EdgesetTable()
ts.dump_tables(nodes=nodes, edgesets=edgesets)
new_nodes = msprime.NodeTable()
names = ["n_{}".format(u) for u in range(ts.num_nodes)]
packed, length = msprime.pack_strings(names)
new_nodes.set_columns(name=packed,
name_length=length,
flags=nodes.flags,
time=nodes.time)
return msprime.load_tables(nodes=new_nodes,
edgesets=edgesets,
provenance_strings=[b"sdf"])
def finalise(self):
if self.genotypes_buffer is None:
raise ValueError("Cannot call finalise in read-mode")
variant_sites = []
num_samples = self.num_samples
num_sites = len(self.site_buffer)
if num_sites == 0:
raise ValueError("Must have at least one site")
position = np.empty(num_sites)
frequency = np.empty(num_sites, dtype=np.uint32)
ancestral_states = []
derived_states = []
for j, site in enumerate(self.site_buffer):
position[j] = site.position
frequency[j] = site.frequency
if site.frequency > 1 and site.frequency < num_samples:
variant_sites.append(j)
ancestral_states.append(site.alleles[0])
derived_states.append(
"" if len(site.alleles) < 2 else site.alleles[1])
sites_group = self.data.create_group("sites")
sites_group.array("position",
data=position,
chunks=(num_sites, ),
compressor=self.compressor)
sites_group.array("frequency",
data=frequency,
chunks=(num_sites, ),
compressor=self.compressor)
ancestral_state, ancestral_state_offset = msprime.pack_strings(
ancestral_states)
sites_group.array("ancestral_state",
data=ancestral_state,
chunks=(num_sites, ),
compressor=self.compressor)
sites_group.array("ancestral_state_offset",
data=ancestral_state_offset,
chunks=(num_sites + 1, ),
compressor=self.compressor)
derived_state, derived_state_offset = msprime.pack_strings(
derived_states)
sites_group.array("derived_state",
data=derived_state,
chunks=(num_sites, ),
compressor=self.compressor)
sites_group.array("derived_state_offset",
data=derived_state_offset,
chunks=(num_sites + 1, ),
compressor=self.compressor)
num_singletons = len(self.singletons_buffer)
singleton_sites = np.array(
[site for site, _ in self.singletons_buffer], dtype=np.int32)
singleton_samples = np.array(
[sample for _, sample in self.singletons_buffer], dtype=np.int32)
singletons_group = self.data.create_group("singletons")
chunks = max(num_singletons, 1),
singletons_group.array("site",
data=singleton_sites,
chunks=chunks,
compressor=self.compressor)
singletons_group.array("sample",
data=singleton_samples,
chunks=chunks,
compressor=self.compressor)
num_invariants = len(self.invariants_buffer)
invariant_sites = np.array(self.invariants_buffer, dtype=np.int32)
invariants_group = self.data.create_group("invariants")
chunks = max(num_invariants, 1),
invariants_group.array("site",
data=invariant_sites,
chunks=chunks,
compressor=self.compressor)
num_variant_sites = len(variant_sites)
self.data.attrs["num_sites"] = num_sites
self.data.attrs["num_variant_sites"] = num_variant_sites
self.data.attrs["num_singleton_sites"] = num_singletons
self.data.attrs["num_invariant_sites"] = num_invariants
chunks = max(num_variant_sites, 1),
self.variants_group.create_dataset("site",
shape=(num_variant_sites, ),
chunks=chunks,
dtype=np.int32,
data=variant_sites,
compressor=self.compressor)
self.genotypes.append(
self.genotypes_buffer[:self.genotypes_buffer_offset])
self.site_buffer = None
self.genotypes_buffer = None
super(SampleData, self).finalise()