def test_reload_annotate(self):
"""
Test the ability of SLiM to load our files after annotation.
"""
for ts, basename in self.get_slim_restarts():
tables = ts.tables
metadata = list(pyslim.extract_mutation_metadata(tables))
has_nucleotides = (metadata[0][0].nucleotide >= 0)
if has_nucleotides:
nucs = [random.choice([0, 1, 2, 3]) for _ in metadata]
refseq = "".join(
random.choices(pyslim.NUCLEOTIDES,
k=int(ts.sequence_length)))
for n, md in zip(nucs, metadata):
for j in range(len(md)):
md[j].nucleotide = n
else:
refseq = None
for md in metadata:
for j in range(len(md)):
md[j].selection_coeff = random.random()
pyslim.annotate_mutation_metadata(tables, metadata)
in_ts = pyslim.load_tables(tables, reference_sequence=refseq)
# put it through SLiM (which just reads in and writes out)
out_ts = self.run_slim_restart(in_ts, basename)
# check for equality, in everything but the last provenance
self.verify_slim_restart_equality(in_ts, out_ts)
def test_annotate_mutations(self):
for ts in self.get_slim_examples():
tables = ts.tables
new_tables = ts.tables
metadata = []
for md in tskit.unpack_bytes(tables.mutations.metadata,
tables.mutations.metadata_offset):
dm = pyslim.decode_mutation(md)
edm = pyslim.encode_mutation(dm)
self.assertEqual(md, edm)
metadata.append(dm)
pyslim.annotate_mutation_metadata(new_tables, metadata)
self.assertEqual(tables, new_tables)
def test_annotate_mutations(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_mutation_metadata(tables))
self.assertEqual(len(metadata), slim_ts.num_mutations)
selcoefs = [random.uniform(0, 1) for _ in metadata]
for j in range(len(metadata)):
metadata[j].selection_coeff = selcoefs[j]
pyslim.annotate_mutation_metadata(tables, metadata)
new_ts = pyslim.load_tables(tables)
for j, x in enumerate(new_ts.mutations()):
md = pyslim.decode_mutation(x.metadata)
self.assertEqual(md.selection_coeff, selcoefs[j])