fast5_to_fastq.py 文件源码

def check_filters(fast5_file, min_length, min_mean_qual, min_qual_window, window_size):
    try:
        hdf5_file = h5py.File(fast5_file, 'r')
        names = get_hdf5_names(hdf5_file)
        basecall_location = get_best_fastq_hdf5_location(hdf5_file, names)
        if basecall_location:
            fastq_str = hdf5_file[basecall_location].value
            try:
                parts = fastq_str.split(b'\n')
                seq, quals = parts[1], parts[3]
            except IndexError:
                fastq_str, seq, quals = '', '', ''
            if not fastq_str or not seq:
                return False, 0
            if min_mean_qual and get_mean_qscore(quals) < min_mean_qual:
                return False, 0
            if min_length and len(seq) < min_length:
                return False, 0
            if min_qual_window and get_min_window_qscore(quals, window_size) < min_qual_window:
                return False, 0
            return True, len(seq)
    except (IOError, RuntimeError):
        pass
    return False, 0