nanoraw_helper.py 文件源码

def get_reads_base_lengths(chrm_strand_reads, chrm_len, rev_strand):
    base_length_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_lengths = read_data[events_slot]['length']

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

    return base_length_sums / base_cov