Example #1
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 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])
Example #3
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)
Example #4
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)