Question

我正在尝试模拟一些dna测序读取，并且为了加速代码，我需要并行运行它。

基本上，我要做的是以下内容：我从人类基因组中抽取读数，我认为来自多处理模块的两个过程试图从同一个文件（人类基因组）中获取数据的过程被破坏，无法获得所需的DNA序列。我尝试了不同的东西，但我对并行编程很新，我无法解决我的问题

当我使用一个核心运行脚本时，它可以正常工作。

这是我调用函数的方式

if __name__ == '__main__':
    jobs = []
    # init the processes
    for i in range(number_of_cores):
        length= 100
        lock = mp.Manager().Lock()
        p = mp.Process(target=simulations.sim_reads,args=(lock,FastaFile, "/home/inigo/msc_thesis/genome_data/hg38.fa",length,paired,results_dir,spawn_reads[i],temp_file_names[i]))
        jobs.append(p)
        p.start()
    for p in jobs:
        p.join()

这是我用来获取读取的函数，每个进程都将数据写入不同的文件。

def sim_single_end(lc,fastafile,chr,chr_pos_start,chr_pos_end,read_length, unique_id):

    lc.acquire()
    left_split_read = fastafile.fetch(chr, chr_pos_end - (read_length / 2), chr_pos_end)
    right_split_read = fastafile.fetch(chr, chr_pos_start, chr_pos_start + (read_length / 2))
    reversed_left_split_read = left_split_read[::-1]
    total_read = reversed_left_split_read + right_split_read
    seq_id = "id:%s-%s|left_pos:%s-%s|right:%s-%s " % (unique_id,chr, int(chr_pos_end - (read_length / 2)), int(chr_pos_end), int(chr_pos_start),int(chr_pos_start + (read_length / 2)))
    quality = "I" * read_length
    fastq_string = "@%s\n%s\n+\n%s\n" % (seq_id, total_read, quality)
    lc.release()
    new_record = SeqIO.read(StringIO(fastq_string), "fastq")
    return(new_record)

这是追溯：

Traceback (most recent call last):
  File "/usr/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap
    self.run()
  File "/usr/lib/python3.5/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/home/inigo/Dropbox/PycharmProjects/circ_dna/simulations.py", line 107, in sim_ecc_reads
   new_read = sim_single_end(lc,fastafile, chr, chr_pos_start, chr_pos_end, read_length, read_id)
   File "/home/inigo/Dropbox/PycharmProjects/circ_dna/simulations.py", line 132, in sim_single_end
   new_record = SeqIO.read(StringIO(fastq_string), "fastq")
   File "/usr/local/lib/python3.5/dist-packages/Bio/SeqIO/__init__.py", line 664, in read
   first = next(iterator)
   File "/usr/local/lib/python3.5/dist-packages/Bio/SeqIO/__init__.py", line 600, in parse
for r in i:
   File "/usr/local/lib/python3.5/dist-packages/Bio/SeqIO/QualityIO.py", line 1031, in FastqPhredIterator
for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
   File "/usr/local/lib/python3.5/dist-packages/Bio/SeqIO/QualityIO.py", line 951, in FastqGeneralIterator
% (title_line, seq_len, len(quality_string)))

 ValueError: Lengths of sequence and quality values differs  for id:6-chr1_KI270707v1_random|left_pos:50511537-50511587|right:50511214-50511264 (0 and 100).

Answer 1

我是近一年前我做过的答案的OP。问题是我用于阅读人类基因组文件（pysam）的软件包失败了。调用多处理时，问题是拼写错误。

作者说，这应该有效：

 p = mp.Process(target=get_fasta, args=(genome_fa,))

注意＆＃39;，＆＃39;确保你传递一个元组

有关详细信息，请参阅https://github.com/pysam-developers/pysam/issues/409

多进程，各种进程读取同一文件

1 个答案: