def test_pedigree_with_gls(): ped = Pedigree(NumericSampleIds()) genotypes1 = [0, 1, 0, 2] gls1 = [ PhredGenotypeLikelihoods(0, 1, 2), PhredGenotypeLikelihoods(215, 81, 147), PhredGenotypeLikelihoods(199, 49, 253), PhredGenotypeLikelihoods(167, 200, 163), ] genotypes5 = [1, 2, 2, 0] gls5 = [ PhredGenotypeLikelihoods(184, 71, 233), PhredGenotypeLikelihoods(65, 32, 87), PhredGenotypeLikelihoods(28, 215, 131), PhredGenotypeLikelihoods(98, 250, 137), ] ped.add_individual('sample1', genotypes1, gls1) assert len(ped) == 1 assert ped.variant_count == 4, str(ped.variant_count) ped.add_individual('sample5', genotypes5, gls5) assert len(ped) == 2 assert ped.variant_count == 4, str(ped.variant_count) for i in range(ped.variant_count): assert ped.genotype('sample1', i) == genotypes1[i] assert list(ped.genotype_likelihoods('sample1', i)) == list(gls1[i]) assert ped.genotype('sample5', i) == genotypes5[i] assert list(ped.genotype_likelihoods('sample5', i)) == list(gls5[i])
def test_pedigree_no_gls(): ped = Pedigree(NumericSampleIds()) genotypes1 = [0, 1, 0, 2] genotypes5 = [1, 2, 2, 0] ped.add_individual('sample1', genotypes1) assert len(ped) == 1 assert ped.variant_count == 4, str(ped.variant_count) ped.add_individual('sample5', genotypes5) assert len(ped) == 2 assert ped.variant_count == 4, str(ped.variant_count) for i in range(ped.variant_count): assert ped.genotype('sample1', i) == genotypes1[i] assert ped.genotype_likelihoods('sample1', i) is None assert ped.genotype('sample5', i) == genotypes5[i] assert ped.genotype_likelihoods('sample5', i) is None