def test_vcf_stats(self):
vcf_stats = VcfStats(VARSCAN_VCF_PATH, min_calls_for_pop_stats=2)
assert vcf_stats.gt_quals(HET)[21] == 2
assert vcf_stats.gt_quals(HOM)[3] == 25
assert vcf_stats.gt_quals(HET).count == 53
assert (0.28 - vcf_stats.heterozigosity_for_sample('pepo')) < 0.01
assert vcf_stats.het_by_snp[0] == 46
fpath = join(TEST_DATA_DIR, 'freebayes6.vcf.gz')
vcf_stats = VcfStats(fpath)
covertures = vcf_stats.depths.keys()
for i in [8, 2, 100, 7]:
assert i in covertures
def test_vcf_stats(self):
vcf_stats = VcfStats(VARSCAN_VCF_PATH, min_calls_for_pop_stats=2)
assert vcf_stats.gt_quals(HET)[21] == 2
assert vcf_stats.gt_quals(HOM)[3] == 25
assert vcf_stats.gt_quals(HET).count == 53
assert (0.28 - vcf_stats.heterozigosity_for_sample('pepo')) < 0.01
assert vcf_stats.het_by_snp[0] == 46
fpath = join(TEST_DATA_DIR, 'freebayes6.vcf.gz')
vcf_stats = VcfStats(fpath)
covertures = vcf_stats.depths.keys()
for i in [8, 2, 100, 7]:
assert i in covertures
def test_only_gt_vcf(self):
vcf_stats = VcfStats(GENERIC_VCF, min_calls_for_pop_stats=2)
vcf_stats.heterozigosity_for_sample('BH_T_122_C4EGEACXX_6_250311606_X4') == 0
def test_only_gt_vcf(self):
vcf_stats = VcfStats(GENERIC_VCF, min_calls_for_pop_stats=2)
sample = 'BH_T_122_C4EGEACXX_6_250311606_X4'
res = vcf_stats.heterozigosity_for_sample(sample)
self.assertAlmostEqual(res, 0.16666666)
def test_only_gt_vcf(self):
vcf_stats = VcfStats(GENERIC_VCF, min_calls_for_pop_stats=2)
sample = 'BH_T_122_C4EGEACXX_6_250311606_X4'
res = vcf_stats.heterozigosity_for_sample(sample)
self.assertAlmostEqual(res, 0.16666666)
