def test_maf(self):
gts = numpy.array([])
varis = VariationsArrays()
varis[GT_FIELD] = gts
mafs = calc_maf(varis, chunk_size=None)
assert mafs.shape == (0,)
mafs = calc_maf(varis)
assert mafs.shape == (0,)
mafs = calc_mac(varis, chunk_size=None)
assert mafs.shape == (0,)
mafs = calc_mac(varis)
assert mafs.shape == (0,)
gts = numpy.array([[[0], [0], [0], [0]], [[0], [0], [1], [1]],
[[0], [0], [0], [1]], [[-1], [-1], [-1], [-1]]])
varis = VariationsArrays()
varis[GT_FIELD] = gts
mafs = calc_maf(varis, min_num_genotypes=1)
assert numpy.allclose(mafs, numpy.array([1., 0.5, 0.75, numpy.NaN]),
equal_nan=True)
macs = calc_mac(varis, min_num_genotypes=1)
assert numpy.allclose(macs, numpy.array([4, 2, 3, numpy.NaN]),
equal_nan=True)
varis = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
mafs = calc_maf(varis)
assert numpy.all(mafs[numpy.logical_not(numpy.isnan(mafs))] >= 0.5)
assert numpy.all(mafs[numpy.logical_not(numpy.isnan(mafs))] <= 1)
assert mafs.shape == (943,)
macs = calc_mac(varis)
# assert macs.shape == (943,)
min_mac = varis['/calls/GT'].shape[1] / 2
max_mac = varis['/calls/GT'].shape[1]
assert numpy.all(macs[numpy.logical_not(numpy.isnan(mafs))] >= min_mac)
assert numpy.all(macs[numpy.logical_not(numpy.isnan(mafs))] <= max_mac)
def test_maf(self):
gts = numpy.array([])
varis = VariationsArrays()
varis[GT_FIELD] = gts
mafs = calc_maf(varis, chunk_size=None)
assert mafs.shape == (0,)
mafs = calc_maf(varis)
assert mafs.shape == (0,)
mafs = calc_mac(varis, chunk_size=None)
assert mafs.shape == (0,)
mafs = calc_mac(varis)
assert mafs.shape == (0,)
gts = numpy.array([[[0], [0], [0], [0]], [[0], [0], [1], [1]],
[[0], [0], [0], [1]], [[-1], [-1], [-1], [-1]]])
varis = VariationsArrays()
varis[GT_FIELD] = gts
mafs = calc_maf(varis, min_num_genotypes=1)
assert numpy.allclose(mafs, numpy.array([1., 0.5, 0.75, numpy.NaN]),
equal_nan=True)
macs = calc_mac(varis, min_num_genotypes=1)
assert numpy.allclose(macs, numpy.array([4, 2, 3, numpy.NaN]),
equal_nan=True)
varis = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
mafs = calc_maf(varis)
assert numpy.all(mafs[numpy.logical_not(numpy.isnan(mafs))] >= 0.5)
assert numpy.all(mafs[numpy.logical_not(numpy.isnan(mafs))] <= 1)
assert mafs.shape == (943,)
macs = calc_mac(varis)
# assert macs.shape == (943,)
min_mac = varis['/calls/GT'].shape[1] / 2
max_mac = varis['/calls/GT'].shape[1]
assert numpy.all(macs[numpy.logical_not(numpy.isnan(mafs))] >= min_mac)
assert numpy.all(macs[numpy.logical_not(numpy.isnan(mafs))] <= max_mac)
def _calc_stat(self, variations):
return calc_mac(variations, min_num_genotypes=self.min_num_genotypes)
def _calc_stat(self, variations):
return calc_mac(variations, min_num_genotypes=self.min_num_genotypes)
