def test_haploid_allele_indices_for_genotype_likelihood_index(self):
for aix in six.moves.xrange(20):
allele_indices = (aix,)
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=1)
self.assertEqual(actual, aix)
def test_haploid_allele_indices_for_genotype_likelihood_index(self):
for aix in xrange(20):
allele_indices = (aix,)
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=1)
self.assertEqual(actual, aix)
def test_diploid_allele_indices_for_genotype_likelihood_index(self):
for aix in range(20):
for bix in range(20):
allele_indices = (aix, bix)
expected = tuple(sorted(allele_indices))
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=2)
self.assertEqual(actual, expected)
def test_diploid_allele_indices_for_genotype_likelihood_index(self):
for aix in xrange(20):
for bix in xrange(20):
allele_indices = (aix, bix)
expected = tuple(sorted(allele_indices))
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=2)
self.assertEqual(actual, expected)
def test_unsupported_allele_indices_for_genotype_likelihood_index(
self, ploidy):
with self.assertRaisesRegexp(NotImplementedError,
'only supported for haploid and diploid'):
variant_utils.allele_indices_for_genotype_likelihood_index(0, ploidy)
def most_likely_allele_indices(self):
"""Returns allele indices for the genotype with the largest likelihood."""
ix = np.argmax(self.scaled_likelihoods())
return variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=2)
def test_unsupported_allele_indices_for_genotype_likelihood_index(
self, ploidy):
with self.assertRaisesRegexp(NotImplementedError,
'only supported for haploid and diploid'):
variant_utils.allele_indices_for_genotype_likelihood_index(0, ploidy)
