def test_annotate_individuals(self):
for ts in self.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 = ind.metadata
self.assertEqual(md.sex, sexes[j])
# try loading this into SLiM
loaded_ts = self.run_msprime_restart(new_ts, sex="A")
self.verify_annotated_tables(new_ts, slim_ts)
self.verify_annotated_trees(new_ts, slim_ts)
self.verify_haplotype_equality(new_ts, slim_ts)
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_XY(self):
for ts in self.get_msprime_examples():
for genome_type in ["X", "Y"]:
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)
node_metadata = list(pyslim.extract_node_metadata(tables))
self.assertEqual(len(node_metadata), slim_ts.num_nodes)
for j in range(slim_ts.num_individuals):
nodes = slim_ts.individual(j).nodes
node_metadata[nodes[0]].genome_type = pyslim.GENOME_TYPE_X
node_metadata[nodes[0]].is_null = (genome_type != "X")
if sexes[j] == pyslim.INDIVIDUAL_TYPE_MALE:
node_metadata[
nodes[1]].genome_type = pyslim.GENOME_TYPE_Y
node_metadata[nodes[1]].is_null = (genome_type != "Y")
else:
node_metadata[
nodes[1]].genome_type = pyslim.GENOME_TYPE_X
node_metadata[nodes[1]].is_null = (genome_type != "X")
pyslim.annotate_node_metadata(tables, node_metadata)
new_ts = pyslim.load_tables(tables)
# try loading this into SLiM
loaded_ts = self.run_msprime_restart(new_ts, sex=genome_type)
self.verify_annotated_tables(new_ts, slim_ts)
self.verify_annotated_trees(new_ts, slim_ts)
self.verify_haplotype_equality(new_ts, slim_ts)
def verify_defaults(self, ts):
'''
Verify the default values have been entered into metadata.
'''
mut_md = pyslim.extract_mutation_metadata(ts.tables)
for md in mut_md:
self.assertEqual(md.mutation_type, 1)
self.assertEqual(md.selection_coeff, 0.0)
self.assertEqual(md.population, tskit.NULL)
self.assertEqual(md.slim_time, 0)
node_md = pyslim.extract_node_metadata(ts.tables)
for md, node in zip(node_md, ts.nodes()):
if not node.is_sample():
self.assertEqual(md, None)
else:
self.assertEqual(md.is_null, False)
self.assertEqual(md.genome_type, pyslim.GENOME_TYPE_AUTOSOME)
for ind in ts.individuals():
self.assertArrayEqual(ind.location, [0, 0, 0])
self.assertEqual(ind.flags, pyslim.INDIVIDUAL_ALIVE)
ind_md = pyslim.extract_individual_metadata(ts.tables)
for md in ind_md:
self.assertEqual(md.sex, pyslim.INDIVIDUAL_TYPE_HERMAPHRODITE)
self.assertEqual(md.flags, 0)
pop_md = pyslim.extract_population_metadata(ts.tables)
for md in pop_md:
self.assertEqual(md.selfing_fraction, 0.0)
self.assertEqual(md.female_cloning_fraction, 0.0)
self.assertEqual(md.male_cloning_fraction, 0.0)
self.assertEqual(md.sex_ratio, 0.5)
self.assertEqual(md.bounds_x0, 0.0)
self.assertEqual(md.bounds_x1, 0.0)
self.assertEqual(md.bounds_y0, 0.0)
self.assertEqual(md.bounds_y1, 0.0)
self.assertEqual(md.bounds_z0, 0.0)
self.assertEqual(md.bounds_z1, 0.0)
self.assertEqual(len(md.migration_records), 0)
# Keywords: Python, nonWF, non-Wright-Fisher, tree-sequence recording, tree sequence recording
import msprime, pyslim, random
ts = msprime.simulate(sample_size=10000, Ne=5000, length=1e8,
mutation_rate=0.0, recombination_rate=1e-8)
tables = ts.dump_tables()
pyslim.annotate_defaults_tables(tables, model_type="nonWF", slim_generation=1)
individual_metadata = list(pyslim.extract_individual_metadata(tables))
for j in range(len(individual_metadata)):
individual_metadata[j].sex = random.choice([pyslim.INDIVIDUAL_TYPE_FEMALE, pyslim.INDIVIDUAL_TYPE_MALE])
individual_metadata[j].age = random.choice([0, 1, 2, 3, 4])
pyslim.annotate_individual_metadata(tables, individual_metadata)
slim_ts = pyslim.load_tables(tables)
slim_ts.dump("recipe_16.9.trees")
# Keywords: Python, nonWF, non-Wright-Fisher, tree-sequence recording, tree sequence recording
import msprime, pyslim, random
ts = msprime.simulate(sample_size=10000, Ne=5000, length=1e8,
mutation_rate=0.0, recombination_rate=1e-8)
tables = ts.dump_tables()
pyslim.annotate_defaults_tables(tables, model_type="nonWF", slim_generation=1)
individual_metadata = list(pyslim.extract_individual_metadata(tables))
for j in range(len(individual_metadata)):
individual_metadata[j].sex = random.choice([pyslim.INDIVIDUAL_TYPE_FEMALE, pyslim.INDIVIDUAL_TYPE_MALE])
individual_metadata[j].age = random.choice([0, 1, 2, 3, 4])
pyslim.annotate_individual_metadata(tables, individual_metadata)
slim_ts = pyslim.load_tables(tables)
slim_ts.dump("recipe_17.9.trees")