def test_simplify_to_sample(self):
"""
Simplify to a sample using fwdpy11 and
tskit, then test that total time on output
is the same from both sources and that
the mutation tables contain the same
positions after simplification.
"""
dumped_ts = self.pop.dump_tables_to_tskit()
tt = 0.0
for i in self.pop.tables.nodes:
tt += i.time
samples = np.arange(0, 2 * self.pop.N, 50, dtype=np.int32)
mspts = dumped_ts.simplify(samples=samples.tolist())
fp11ts, idmap = fwdpy11.simplify(self.pop, samples)
for i in range(len(fp11ts.edges)):
self.assertTrue(fp11ts.edges[i].parent < len(fp11ts.nodes))
self.assertTrue(fp11ts.edges[i].child < len(fp11ts.nodes))
for s in samples:
self.assertEqual(fp11ts.nodes[idmap[s]].time, self.pop.generation)
tt_fwd = 0.0
tv = fwdpy11.TreeIterator(fp11ts, [i for i in range(len(samples))])
for t in tv:
tt_fwd += t.total_time(fp11ts.nodes)
tt_tskit = 0.0
for t in mspts.trees():
tt_tskit += t.get_total_branch_length()
self.assertEqual(tt_fwd, tt_tskit)
self.assertEqual(len(fp11ts.mutations), len(mspts.tables.mutations))
fp11_pos = np.array(
[self.pop.mutations[i.key].pos for i in fp11ts.mutations])
fp11_pos = np.sort(fp11_pos)
msp_pos = np.sort(mspts.tables.sites.position)
self.assertTrue(np.array_equal(fp11_pos, msp_pos))
def test_simplify_numpy_array(self):
tables, idmap = fwdpy11.simplify(self.pop,
np.array([i for i in range(10)]))
for i in range(10):
self.assertTrue(idmap[i] != fwdpy11.NULL_NODE)
def test_simplify(self):
tables, idmap = fwdpy11.simplify(self.pop, [i for i in range(10)])
for i in range(10):
self.assertTrue(idmap[i] != fwdpy11.NULL_NODE)