def test_genotype_confidence_setter(self):
dummy_vcfgenotypeinfo = ns_test.VCFGenotypeInfo('')
dummy_vcfgenotypeinfo.genotype_confidence = "89"
self.assertEqual(89.0, dummy_vcfgenotypeinfo.genotype_confidence)
dummy_vcfgenotypeinfo.genotype_confidence = 89
self.assertEqual(89.0, dummy_vcfgenotypeinfo.genotype_confidence)
dummy_vcfgenotypeinfo.genotype_confidence = "-89.10"
self.assertEqual(-89.1, dummy_vcfgenotypeinfo.genotype_confidence)
def test_fill_unfiltered_reads_counts(self):
genotype_to_fill = ns_test.VCFGenotypeInfo('')
ns_test._fill_unfiltered_reads_counts('0,64,12', genotype_to_fill)
self.assertEqual(3, len(genotype_to_fill.alleles))
self.assertEqual(0, genotype_to_fill.alleles[0].unfiltered_read_counts)
self.assertEqual(64,
genotype_to_fill.alleles[1].unfiltered_read_counts)
self.assertEqual(12,
genotype_to_fill.alleles[2].unfiltered_read_counts)
def test_filter_passing_reads_count_setter(self):
dummy_vcfgenotypeinfo = ns_test.VCFGenotypeInfo('')
dummy_vcfgenotypeinfo.filter_passing_reads_count = "42"
self.assertEqual(42, dummy_vcfgenotypeinfo.filter_passing_reads_count)
dummy_vcfgenotypeinfo.filter_passing_reads_count = 0
self.assertEqual(0, dummy_vcfgenotypeinfo.filter_passing_reads_count)
dummy_vcfgenotypeinfo.filter_passing_reads_count = "."
self.assertEqual(None,
dummy_vcfgenotypeinfo.filter_passing_reads_count)
def test_fill_unfiltered_reads_counts_warn(self):
genotype_to_fill = ns_test.VCFGenotypeInfo('')
with warnings.catch_warnings(record=True) as w:
genotype_to_fill = ns_test._fill_unfiltered_reads_counts(
'0;64', genotype_to_fill)
self.assertEqual(
"The AD tag value 0;64 does not split into at least two values so unfiltered allele depth"
" information could not be captured for the current variant.",
_help_get_warn_msg(w))
self.assertEqual(0, len(genotype_to_fill.alleles)
) # no alleles created if AD tag splits wrong
def test_fill_genotype_warn(self):
genotype_to_fill = ns_test.VCFGenotypeInfo('')
with warnings.catch_warnings(record=True) as w:
genotype_to_fill = ns_test._fill_genotype('1/0/2',
genotype_to_fill)
self.assertEqual(
"The GT tag value 1/0/2 does not split into exactly two values so genotype information "
"could not be captured for the current variant.",
_help_get_warn_msg(w))
self.assertIsNone(genotype_to_fill.genotype
) # no genotype created if GT tag splits wrong
def test_fill_genotype_likelihoods_warn_too_many_alleles_implied(self):
genotype_to_fill = ns_test.VCFGenotypeInfo('')
genotype_to_fill.alleles = [
ns_test.Allele(10),
ns_test.Allele(11),
ns_test.Allele(12)
]
with warnings.catch_warnings(record=True) as w:
genotype_to_fill = ns_test._fill_genotype_likelihoods(
'495,162,123,213,129,175,67,0,46,28.1', genotype_to_fill)
self.assertEqual(
"The PL tag value 495,162,123,213,129,175,67,0,46,28.1 appears to contain information for "
"more alleles than expected so 'normalized' Phred-scaled likelihoods of possible genotypes"
" information could not be captured for the current variant.",
_help_get_warn_msg(w))
self.assertEqual(0, len(genotype_to_fill.genotype_likelihoods)
) # no likelihoods made if PL splits wrong
def test_fill_genotype_likelihoods_no_alleles(self):
expected_values = [(0, 0, 495), (0, 1, 162), (1, 1, 123)]
genotype_to_fill = ns_test.VCFGenotypeInfo('')
self.assertEqual(0, len(genotype_to_fill.alleles))
ns_test._fill_genotype_likelihoods('495,162,123', genotype_to_fill)
self.assertEqual(2, len(
genotype_to_fill.alleles)) # should have added two
self.assertEqual(len(expected_values),
len(genotype_to_fill.genotype_likelihoods))
for index in range(0, len(expected_values)):
curr_expected_values = expected_values[index]
real_values = genotype_to_fill.genotype_likelihoods[index]
self.assertEqual(curr_expected_values[0],
real_values.allele1_number)
self.assertEqual(curr_expected_values[1],
real_values.allele2_number)
self.assertEqual(curr_expected_values[2],
real_values.likelihood_neg_exponent)
def test_fill_genotype_likelihoods_three_alleles(self):
expected_values = [(0, 0, 495), (0, 1, 162), (1, 1, 123), (0, 2, 213),
(1, 2, 129), (2, 2, 175), (0, 3, 67), (1, 3, 0),
(2, 3, 46), (3, 3, 28.1)]
genotype_to_fill = ns_test.VCFGenotypeInfo('')
genotype_to_fill.alleles = [
ns_test.Allele(10),
ns_test.Allele(11),
ns_test.Allele(12),
ns_test.Allele(13)
]
ns_test._fill_genotype_likelihoods(
'495,162,123,213,129,175,67,0,46,28.1', genotype_to_fill)
self.assertEqual(len(expected_values),
len(genotype_to_fill.genotype_likelihoods))
for index in range(0, len(expected_values)):
curr_expected_values = expected_values[index]
real_values = genotype_to_fill.genotype_likelihoods[index]
self.assertEqual(curr_expected_values[0],
real_values.allele1_number)
self.assertEqual(curr_expected_values[1],
real_values.allele2_number)
self.assertEqual(curr_expected_values[2],
real_values.likelihood_neg_exponent)
def test_fill_genotype_confidence(self):
genotype_to_fill = ns_test.VCFGenotypeInfo('')
ns_test._fill_genotype_confidence('44.1', genotype_to_fill)
self.assertEqual(44.1, genotype_to_fill.genotype_confidence)
def test_fill_filtered_reads_count(self):
genotype_to_fill = ns_test.VCFGenotypeInfo('')
ns_test._fill_filtered_reads_count('44', genotype_to_fill)
self.assertEqual(44, genotype_to_fill.filter_passing_reads_count)
def test_filter_passing_reads_count_setter_error(self):
dummy_vcfgenotypeinfo = ns_test.VCFGenotypeInfo('')
with self.assertRaises(ValueError):
dummy_vcfgenotypeinfo.filter_passing_reads_count = -1
with self.assertRaises(ValueError):
dummy_vcfgenotypeinfo.filter_passing_reads_count = 48.5
def test_genotype_confidence_setter_error(self):
dummy_vcfgenotypeinfo = ns_test.VCFGenotypeInfo('')
with self.assertRaises(ValueError):
dummy_vcfgenotypeinfo.genotype_confidence = "blue"
def test_fill_genotype(self):
genotype_to_fill = ns_test.VCFGenotypeInfo('')
ns_test._fill_genotype('0/2', genotype_to_fill)
self.assertEqual('0/2', genotype_to_fill.genotype)
