Python calc_stat_by_chunk Examples

Example #1

def stats_mafs_from_hdf5():
    fpath = join(TEST_DATA_DIR, 'performance', 'inca_torvum_all_snps.h5')
    h5 = VariationsH5(fpath, mode='r')
    calc_stat_by_chunk(h5, _MafCalculator())

Example #2

File: performance.py Project: JoseBlanca/variation

def stats_mafs_from_hdf5():
    fpath = join(TEST_DATA_DIR, 'performance', 'inca_torvum_all_snps.h5')
    h5 = VariationsH5(fpath, mode='r')
    calc_stat_by_chunk(h5, _MafCalculator())

Example #3

def stats_missing_rate_from_hdf5_memory():
    fpath = join(TEST_DATA_DIR, 'performance', 'inca_torvum_all_snps.h5')
    var_mat = VariationsH5(fpath, mode='r')
    array = VariationsArrays()
    array.put_chunks(var_mat.iterate_chunks(kept_fields=['/calls/GT']))
    calc_stat_by_chunk(array, _MissingGTCalculator())

Example #4

File: performance.py Project: JoseBlanca/variation

def stats_missing_rate_from_hdf5_memory():
    fpath = join(TEST_DATA_DIR, 'performance', 'inca_torvum_all_snps.h5')
    var_mat = VariationsH5(fpath, mode='r')
    array = VariationsArrays()
    array.put_chunks(var_mat.iterate_chunks(kept_fields=['/calls/GT']))
    calc_stat_by_chunk(array, _MissingGTCalculator())