def test_calc_obs_het(self):
gts = numpy.array([])
dps = numpy.array([])
varis = {'/calls/GT': gts, '/calls/DP': dps}
het = calc_obs_het(varis, min_num_genotypes=0)
assert het.shape[0] == 0
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
snps = VariationsArrays()
snps.put_chunks(hdf5.iterate_chunks(kept_fields=['/calls/GT']))
het_h5 = calc_obs_het(hdf5, min_num_genotypes=0)
het_array = calc_obs_het(snps, min_num_genotypes=0)
assert numpy.all(het_array == het_h5)
gts = numpy.array([[[0, 0], [0, 1], [0, -1], [-1, -1]],
[[0, 0], [0, 0], [0, -1], [-1, -1]]])
dps = numpy.array([[5, 12, 10, 10],
[10, 10, 10, 10]])
varis = {'/calls/GT': gts, '/calls/DP': dps}
het = calc_obs_het(varis, min_num_genotypes=0)
assert numpy.allclose(het, [0.5, 0])
het = calc_obs_het(varis, min_num_genotypes=10)
assert numpy.allclose(het, [numpy.NaN, numpy.NaN], equal_nan=True)
het = calc_obs_het(varis, min_num_genotypes=0, min_call_dp=10)
assert numpy.allclose(het, [1, 0])
het = calc_obs_het(varis, min_num_genotypes=0, max_call_dp=11)
assert numpy.allclose(het, [0, 0])
het = calc_obs_het(varis, min_num_genotypes=0, min_call_dp=5)
assert numpy.allclose(het, [0.5, 0])
def test_calc_obs_het(self):
gts = numpy.array([])
dps = numpy.array([])
varis = {'/calls/GT': gts, '/calls/DP': dps}
het = calc_obs_het(varis, min_num_genotypes=0)
assert het.shape[0] == 0
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
snps = VariationsArrays()
snps.put_chunks(hdf5.iterate_chunks(kept_fields=['/calls/GT']))
het_h5 = calc_obs_het(hdf5, min_num_genotypes=0)
het_array = calc_obs_het(snps, min_num_genotypes=0)
assert numpy.all(het_array == het_h5)
gts = numpy.array([[[0, 0], [0, 1], [0, -1], [-1, -1]],
[[0, 0], [0, 0], [0, -1], [-1, -1]]])
dps = numpy.array([[5, 12, 10, 10],
[10, 10, 10, 10]])
varis = {'/calls/GT': gts, '/calls/DP': dps}
het = calc_obs_het(varis, min_num_genotypes=0)
assert numpy.allclose(het, [0.5, 0])
het = calc_obs_het(varis, min_num_genotypes=10)
assert numpy.allclose(het, [numpy.NaN, numpy.NaN], equal_nan=True)
het = calc_obs_het(varis, min_num_genotypes=0, min_call_dp=10)
assert numpy.allclose(het, [1, 0])
het = calc_obs_het(varis, min_num_genotypes=0, max_call_dp=11)
assert numpy.allclose(het, [0, 0])
het = calc_obs_het(varis, min_num_genotypes=0, min_call_dp=5)
assert numpy.allclose(het, [0.5, 0])
def _calc_stat(self, variations):
return calc_obs_het(variations,
min_num_genotypes=self.min_num_genotypes,
min_call_dp=self.min_call_dp)
def _calc_stat(self, variations):
return calc_obs_het(variations,
min_num_genotypes=self.min_num_genotypes,
min_call_dp=self.min_call_dp)