rnaMaskingStep.py 文件源码

def maskRibosomalSequence(seqRecord, dict16S, dict23S, dict5S, dict_t_rna):
    passed = False
    seq = seqRecord.seq
    id = seqRecord.id
    dicts = [dict16S, dict23S, dict5S, dict_t_rna]

    for d in dicts:
        if id in d:
            start_pos = d[id][1]
            end_pos = d[id][2]
            seq_length = d[id][0]
            logging.debug("identifier: " + id)
            logging.debug("Start : " + str(start_pos))
            logging.debug("End   : " + str(end_pos))
            logging.debug("Length: " + str(seq_length))
            logging.debug("original sequence: " + seq)
            # mask the RNA regions
            seq = seq[:int(start_pos) - 1] + "N" * (int(end_pos) - int(start_pos) + 1) + seq[
                                                                                         int(end_pos):int(seq_length)]
            logging.debug("masked sequence  : " + seq)
    # write the resulting masked sequences to file
    if len(str(seq).replace("N", "")) > 60:
        seqRecord.seq = seq
        passed = True
    return seqRecord, passed