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Merge pull request #110 from szhan/split_tests_by_algo
Split tests by algorithm
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| import pytest | ||
|
|
||
| from . import lsbase | ||
| import lshmm as ls | ||
| import lshmm.core as core | ||
| import lshmm.vit_diploid as vd | ||
|
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||
|
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| class TestViterbiDiploid(lsbase.ViterbiAlgorithmBase): | ||
| def verify(self, ts, scale_mutation_rate, include_ancestors): | ||
| for n, m, H_vs, query, e_vs, r, mu in self.get_examples_pars( | ||
| ts, | ||
| ploidy=2, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| include_ancestors=include_ancestors, | ||
| include_extreme_rates=True, | ||
| ): | ||
| G_vs = core.convert_haplotypes_to_phased_genotypes(H_vs) | ||
| s = core.convert_haplotypes_to_unphased_genotypes(query) | ||
| num_alleles = core.get_num_alleles(H_vs, query) | ||
|
|
||
| V_vs, P_vs, ll_vs = vd.forwards_viterbi_dip_low_mem( | ||
| n=n, | ||
| m=m, | ||
| G=G_vs, | ||
| s=s, | ||
| e=e_vs, | ||
| r=r, | ||
| ) | ||
| path_vs = vd.backwards_viterbi_dip(m=m, V_last=V_vs, P=P_vs) | ||
| phased_path_vs = vd.get_phased_path(n=n, path=path_vs) | ||
| path, ll = ls.viterbi( | ||
| reference_panel=G_vs, | ||
| query=s, | ||
| num_alleles=num_alleles, | ||
| prob_recombination=r, | ||
| prob_mutation=mu, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| ) | ||
|
|
||
| self.assertAllClose(ll_vs, ll) | ||
| self.assertAllClose(phased_path_vs, path) | ||
|
|
||
| @pytest.mark.parametrize("scale_mutation_rate", [True, False]) | ||
| @pytest.mark.parametrize("include_ancestors", [True, False]) | ||
| def test_ts_simple_n10_no_recomb(self, scale_mutation_rate, include_ancestors): | ||
| ts = self.get_ts_simple_n10_no_recomb() | ||
| self.verify( | ||
| ts, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| include_ancestors=include_ancestors, | ||
| ) | ||
|
|
||
| @pytest.mark.parametrize("scale_mutation_rate", [True, False]) | ||
| @pytest.mark.parametrize("include_ancestors", [True, False]) | ||
| def test_ts_simple_n6(self, scale_mutation_rate, include_ancestors): | ||
| ts = self.get_ts_simple_n6() | ||
| self.verify( | ||
| ts, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| include_ancestors=include_ancestors, | ||
| ) | ||
|
|
||
| @pytest.mark.parametrize("scale_mutation_rate", [True, False]) | ||
| @pytest.mark.parametrize("include_ancestors", [True, False]) | ||
| def test_ts_simple_n8(self, scale_mutation_rate, include_ancestors): | ||
| ts = self.get_ts_simple_n8() | ||
| self.verify( | ||
| ts, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| include_ancestors=include_ancestors, | ||
| ) | ||
|
|
||
| @pytest.mark.parametrize("scale_mutation_rate", [True, False]) | ||
| @pytest.mark.parametrize("include_ancestors", [True, False]) | ||
| def test_ts_simple_n8_high_recomb(self, scale_mutation_rate, include_ancestors): | ||
| ts = self.get_ts_simple_n8_high_recomb() | ||
| self.verify( | ||
| ts, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| include_ancestors=include_ancestors, | ||
| ) | ||
|
|
||
| @pytest.mark.parametrize("scale_mutation_rate", [True, False]) | ||
| @pytest.mark.parametrize("include_ancestors", [True, False]) | ||
| def test_ts_simple_n16(self, scale_mutation_rate, include_ancestors): | ||
| ts = self.get_ts_simple_n16() | ||
| self.verify( | ||
| ts, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| include_ancestors=include_ancestors, | ||
| ) | ||
|
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||
| @pytest.mark.parametrize("scale_mutation_rate", [True, False]) | ||
| @pytest.mark.parametrize("include_ancestors", [True, False]) | ||
| def test_ts_larger(self, scale_mutation_rate, include_ancestors): | ||
| ts = self.get_ts_custom_pars( | ||
| ref_panel_size=45, length=1e5, mean_r=1e-5, mean_mu=1e-5 | ||
| ) | ||
| self.verify( | ||
| ts, | ||
| scale_mutation_rate=scale_mutation_rate, | ||
| include_ancestors=include_ancestors, | ||
| ) |
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