def test_set_tree_sequence_metadata_keeps(self):
# make sure doesn't overwrite other stuff
dummy_schema = tskit.MetadataSchema({
'codec': 'json',
'type': 'object',
'properties': {
'abc': {
'type': 'string'
}
}
})
dummy_metadata = {'abc': 'foo'}
for ts in self.get_slim_examples():
tables = ts.tables
tables.metadata_schema = dummy_schema
tables.metadata = dummy_metadata
pyslim.set_tree_sequence_metadata(tables, "nonWF", 0)
schema = tables.metadata_schema.schema
for k in dummy_metadata:
self.assertTrue(k in schema['properties'])
self.assertTrue(k in tables.metadata)
self.assertEqual(tables.metadata[k], dummy_metadata[k])
self.validate_slim_metadata(tables)
self.assertEqual(tables.metadata['SLiM']['model_type'], "nonWF")
self.assertEqual(tables.metadata['SLiM']['generation'], 0)
break
def test_set_tree_sequence_metadata_errors(self):
for ts in self.get_slim_examples():
tables = ts.tables
tables.metadata_schema = tskit.MetadataSchema(None)
self.assertGreater(len(tables.metadata), 0)
with self.assertRaises(ValueError):
pyslim.set_tree_sequence_metadata(tables, "nonWF", 0)
break
def test_set_tree_sequence_metadata(self, recipe):
tables = recipe["ts"].dump_tables()
pyslim.set_tree_sequence_metadata(tables,
"WF",
99,
spatial_dimensionality='xy',
spatial_periodicity='y',
separate_sexes=False,
nucleotide_based=True)
self.validate_slim_metadata(tables)
assert tables.metadata['SLiM']['model_type'] == "WF"
assert tables.metadata['SLiM']['generation'] == 99
assert tables.metadata['SLiM']['spatial_dimensionality'] == 'xy'
assert tables.metadata['SLiM']['spatial_periodicity'] == 'y'
assert tables.metadata['SLiM']['separate_sexes'] == False
assert tables.metadata['SLiM']['nucleotide_based'] == True
def test_set_tree_sequence_metadata(self):
for ts in self.get_slim_examples():
tables = ts.tables
pyslim.set_tree_sequence_metadata(
tables, "WF", 99,
spatial_dimensionality='xy',
spatial_periodicity='y',
separate_sexes=False,
nucleotide_based=True)
self.validate_slim_metadata(tables)
self.assertEqual(tables.metadata['SLiM']['model_type'], "WF")
self.assertEqual(tables.metadata['SLiM']['generation'], 99)
self.assertEqual(tables.metadata['SLiM']['spatial_dimensionality'], 'xy')
self.assertEqual(tables.metadata['SLiM']['spatial_periodicity'], 'y')
self.assertEqual(tables.metadata['SLiM']['separate_sexes'], False)
self.assertEqual(tables.metadata['SLiM']['nucleotide_based'], True)
break
def test_set_tree_sequence_metadata_keeps(self, recipe):
# make sure doesn't overwrite other stuff
for x in [{}, {'properties': {'abc': {'type': 'string'}}}]:
schema_dict = {
'codec': 'json',
'type': 'object',
}
schema_dict.update(x)
dummy_schema = tskit.MetadataSchema(schema_dict)
dummy_metadata = {'abc': 'foo'}
tables = recipe["ts"].dump_tables()
tables.metadata_schema = dummy_schema
tables.metadata = dummy_metadata
pyslim.set_tree_sequence_metadata(tables, "nonWF", 0)
schema = tables.metadata_schema.schema
for k in dummy_metadata:
if len(x) > 0:
assert k in schema['properties']
assert k in tables.metadata
assert tables.metadata[k] == dummy_metadata[k]
self.validate_slim_metadata(tables)
assert tables.metadata['SLiM']['model_type'] == "nonWF"
assert tables.metadata['SLiM']['generation'] == 0
def test_set_tree_sequence_metadata_errors(self, recipe):
tables = recipe["ts"].dump_tables()
tables.metadata_schema = tskit.MetadataSchema(None)
assert len(tables.metadata) > 0
with pytest.raises(ValueError):
pyslim.set_tree_sequence_metadata(tables, "nonWF", 0)
def test_known_answer(self):
# a simple example to make sure we've got the edge cases right
tables = tskit.TableCollection(sequence_length=1)
pyslim.set_tree_sequence_metadata(tables,
model_type='nonWF',
generation=0)
pyslim.set_metadata_schemas(tables)
locs = [
[0, 0], # alive at 0, 1
[0, 1], # alive at 0, 1, 2
[2, 0], # alive at 0, 1, 2
[1, 1], # alive at 0, 1, 2
[0, 0], # alive at 1
[0.5, 1], # alive at 1
[2, 2], # alive at 1
[3, 2] # alive at 0, 1, 2, 3
]
births = [1, 2, 2, 2, 1, 1, 1, 3]
ages = [1, 2, 2, 2, 0, 0, 0, 3]
x_bins = [0, 1, 3]
for xy, a in zip(locs, ages):
md = pyslim.default_slim_metadata('individual')
md['age'] = a
tables.individuals.add_row(
location=xy + [np.nan],
metadata=md,
)
for j, b in enumerate(births):
tables.nodes.add_row(time=b, individual=j)
ts = pyslim.SlimTreeSequence(tables.tree_sequence())
# check we've got this right
for k, n in enumerate([[0, 1, 2, 3, 7], [0, 1, 2, 3, 4, 5, 6, 7],
[1, 2, 3, 7], [7]]):
np.testing.assert_array_equal(n, ts.individuals_alive_at(k))
# no-one
counts = pyslim.population_size(
ts,
x_bins=np.arange(10),
y_bins=np.arange(10),
time_bins=[100, 200, 300],
)
np.testing.assert_array_equal(
counts,
np.zeros((9, 9, 2)),
)
# everyone at the start
counts = pyslim.population_size(
ts,
x_bins=[0, 10],
y_bins=[0, 10],
time_bins=[0, 1],
)
np.testing.assert_array_equal(counts, [[[5]]])
# should omit the last one
counts = pyslim.population_size(ts,
x_bins=[0, 3],
y_bins=[0, 3],
time_bins=[0, 1])
np.testing.assert_array_equal(counts, [[[4]]])
# now should omit the ones at the boundaries
counts = pyslim.population_size(ts,
x_bins=[0, 1, 2],
y_bins=[0, 1, 2],
time_bins=[0, 1, 2, 5])
np.testing.assert_array_equal(
counts, [[[1, 2, 0], [1, 2, 1 / 3]], [[0, 0, 0], [1, 1, 1 / 3]]])