nanoraw_helper.py 文件源码

def get_reads_base_sds(chrm_strand_reads, chrm_len, rev_strand):
    base_sd_sums = np.zeros(chrm_len)
    base_cov = np.zeros(chrm_len, dtype=np.int_)
    for r_data in chrm_strand_reads:
        # extract read means data so data across all chrms is not
        # in RAM at one time
        try:
            read_data = h5py.File(r_data.fn, 'r')
        except IOError:
            # probably truncated file
            continue
        events_slot = '/'.join((
            '/Analyses', r_data.corr_group, 'Events'))
        if events_slot not in read_data:
            continue
        read_sds = read_data[events_slot]['norm_stdev']

        if rev_strand:
            read_sds = read_sds[::-1]
        base_sd_sums[r_data.start:
                     r_data.start + len(read_sds)] += read_sds
        base_cov[r_data.start:r_data.start + len(read_sds)] += 1

    return base_sd_sums / base_cov