How to use the tsinfer.verify function in tsinfer

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github tskit-dev / tsinfer / tests / test_inference.py View on Github external
def test_bad_genotypes(self):
        n = 2
        ts = msprime.simulate(n, mutation_rate=5, random_seed=1)
        self.assertGreater(ts.num_sites, 1)
        with tsinfer.SampleData(sequence_length=ts.sequence_length) as samples:
            for var in ts.variants():
                samples.add_site(
                    position=var.site.position, alleles=var.alleles, genotypes=[0, 0]
                )

        with self.assertRaises(ValueError):
            tsinfer.verify(samples, ts)
github tskit-dev / tsinfer / tests / test_inference.py View on Github external
def test_bad_num_samples(self):
        n = 5
        ts = msprime.simulate(n, mutation_rate=5, random_seed=1)
        self.assertGreater(ts.num_sites, 1)
        with tsinfer.SampleData() as samples:
            for j in range(ts.num_sites):
                samples.add_site(j, genotypes=[0, 1])

        with self.assertRaises(ValueError):
            tsinfer.verify(samples, ts)
github tskit-dev / tsinfer / tests / test_evaluation.py View on Github external
def verify_from_source(self, remove_leaves):
        ts = msprime.simulate(15, recombination_rate=1, mutation_rate=2, random_seed=3)
        samples = tsinfer.SampleData.from_tree_sequence(ts)
        ancestors_ts = tsinfer.make_ancestors_ts(
            samples, ts, remove_leaves=remove_leaves
        )
        tsinfer.check_ancestors_ts(ancestors_ts)
        for engine in [tsinfer.PY_ENGINE, tsinfer.C_ENGINE]:
            final_ts = tsinfer.match_samples(samples, ancestors_ts, engine=engine)
        tsinfer.verify(samples, final_ts)
github tskit-dev / tsinfer / tests / test_inference.py View on Github external
def test_nominal_case(self):
        ts = msprime.simulate(10, mutation_rate=5, random_seed=1)
        self.assertGreater(ts.num_sites, 0)
        samples = tsinfer.SampleData.from_tree_sequence(ts)
        inferred_ts = tsinfer.infer(samples)

        tsinfer.verify(samples, inferred_ts)
        tsinfer.verify(samples, ts)
github tskit-dev / tsinfer / tests / test_evaluation.py View on Github external
def verify_from_inferred(self, remove_leaves):
        ts = msprime.simulate(15, recombination_rate=1, mutation_rate=2, random_seed=3)
        samples = tsinfer.SampleData.from_tree_sequence(ts)
        inferred = tsinfer.infer(samples)
        ancestors_ts = tsinfer.make_ancestors_ts(
            samples, inferred, remove_leaves=remove_leaves
        )
        tsinfer.check_ancestors_ts(ancestors_ts)
        for engine in [tsinfer.PY_ENGINE, tsinfer.C_ENGINE]:
            final_ts = tsinfer.match_samples(samples, ancestors_ts, engine=engine)
        tsinfer.verify(samples, final_ts)
github tskit-dev / tsinfer / tests / test_inference.py View on Github external
def verify(self, samples):
        ts = tsinfer.infer(samples, simplify=False)
        ancestors_ts_1 = self.insert_srb_ancestors(samples, ts)
        ancestors_ts_2 = tsinfer.insert_srb_ancestors(samples, ts)
        t1 = ancestors_ts_1.dump_tables()
        t2 = ancestors_ts_2.dump_tables()
        t1.provenances.clear()
        t2.provenances.clear()
        self.assertEqual(t1, t2)

        tsinfer.check_ancestors_ts(ancestors_ts_1)
        ts2 = tsinfer.match_samples(samples, ancestors_ts_1)
        tsinfer.verify(samples, ts2)
github tskit-dev / tsinfer / tests / test_inference.py View on Github external
def test_bad_num_sites(self):
        n = 2
        ts = msprime.simulate(n, mutation_rate=5, random_seed=1)
        self.assertGreater(ts.num_sites, 1)
        with tsinfer.SampleData() as samples:
            samples.add_site(0, genotypes=[0, 1])

        with self.assertRaises(ValueError):
            tsinfer.verify(samples, ts)
github tskit-dev / tsinfer / dev.py View on Github external
# print("edges before = ", simplified.num_edges)

    # new_ancestors_ts = insert_srb_ancestors(ts)
    # ts = tsinfer.match_samples(samples, new_ancestors_ts,
    #         path_compression=False, engine=engine,
    #         simplify=True)

    #     for tree in ts.trees():
    #         print(tree.interval)
    #         print(tree.draw(format="unicode"))

    # print(ts.tables.edges)
    # for tree in ts.trees():
    #     print(tree.draw(format="unicode"))

    tsinfer.verify(samples, ts)