def MutsFromTrees(Trees):
print('read trees')
ts = pyslim.load(Trees).simplify()
variants = []
# for variant in pyslim.extract_mutation_metadata(ts.tables):
# print(variant)
# return
for variant, mut, node in zip(ts.variants(),
pyslim.extract_mutation_metadata(ts.tables),
pyslim.extract_node_metadata(ts.tables)):
# print ()
# print (variant)
# print (mut)
# print (node)
freq = sum(variant.genotypes) / len(variant.genotypes)
# print (freq)
if freq >= 1: continue
if len(mut) > 1: pass
variants.append([variant.site.position, freq, mut[0].selection_coeff])
return variants
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_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)