子流程中有多个管道

问题描述

我正在尝试在一个ruffus管道中使用Sailfish，它使用多个fastq文件作为参数.我使用python中的子进程模块执行Sailfish，但是即使设置了shell=True，子进程调用中的<()也无法正常工作.

I am trying to use Sailfish, which takes multiple fastq files as arguments, in a ruffus pipeline. I execute Sailfish using the subprocess module in python, but <() in the subprocess call does not work even when I set shell=True.

这是我要使用python执行的命令:

This is the command I want to execute using python:

sailfish quant [options] -1 <(cat sample1a.fastq sample1b.fastq) -2 <(cat sample2a.fastq sample2b.fastq) -o [output_file]

或(最好):

sailfish quant [options] -1 <(gunzip sample1a.fastq.gz sample1b.fastq.gz) -2 <(gunzip sample2a.fastq.gz sample2b.fastq.gz) -o [output_file]

概括:

someprogram <(someprocess) <(someprocess)

我将如何在python中执行此操作?子过程是正确的方法吗?

How would I go about doing this in python? Is subprocess the right approach?

推荐答案

要模拟 bash进程替换:

#!/usr/bin/env python
from subprocess import check_call

check_call('someprogram <(someprocess) <(anotherprocess)',
           shell=True, executable='/bin/bash')

在Python中，您可以使用命名管道:

In Python, you could use named pipes:

#!/usr/bin/env python
from subprocess import Popen

with named_pipes(n=2) as paths:
    someprogram = Popen(['someprogram'] + paths)
    processes = []
    for path, command in zip(paths, ['someprocess', 'anotherprocess']):
        with open(path, 'wb', 0) as pipe:
            processes.append(Popen(command, stdout=pipe, close_fds=True))
    for p in [someprogram] + processes:
        p.wait()

其中named_pipes(n)是:

import os
import shutil
import tempfile
from contextlib import contextmanager

@contextmanager
def named_pipes(n=1):
    dirname = tempfile.mkdtemp()
    try:
        paths = [os.path.join(dirname, 'named_pipe' + str(i)) for i in range(n)]
        for path in paths:
            os.mkfifo(path)
        yield paths
    finally:
        shutil.rmtree(dirname)

---

实现bash进程替换的另一种更可取的方式(无需在磁盘上创建命名条目)是将/dev/fd/N文件名(如果可用)用作.在FreeBSD上， fdescfs(5) ( /dev/fd/#)为该进程打开的所有文件描述符创建条目.要测试可用性，请运行:

---

Another and more preferable way (no need to create a named entry on disk) to implement the bash process substitution is to use /dev/fd/N filenames (if they are available) as suggested by @Dunes. On FreeBSD, fdescfs(5) (/dev/fd/#) creates entries for all file descriptors opened by the process. To test availability, run:

$ test -r /dev/fd/3 3</dev/null && echo /dev/fd is available

如果失败；尝试将/dev/fd符号链接到 proc(5) 在某些Linux上完成:

If it fails; try to symlink /dev/fd to proc(5) as it is done on some Linuxes:

$ ln -s /proc/self/fd /dev/fd

这是someprogram <(someprocess) <(anotherprocess) bash命令的基于/dev/fd的实现:

Here's /dev/fd-based implementation of someprogram <(someprocess) <(anotherprocess) bash command:

#!/usr/bin/env python3
from contextlib import ExitStack
from subprocess import CalledProcessError, Popen, PIPE

def kill(process):
    if process.poll() is None: # still running
        process.kill()

with ExitStack() as stack: # for proper cleanup
    processes = []
    for command in [['someprocess'], ['anotherprocess']]:  # start child processes
        processes.append(stack.enter_context(Popen(command, stdout=PIPE)))
        stack.callback(kill, processes[-1]) # kill on someprogram exit

    fds = [p.stdout.fileno() for p in processes]
    someprogram = stack.enter_context(
        Popen(['someprogram'] + ['/dev/fd/%d' % fd for fd in fds], pass_fds=fds))
    for p in processes: # close pipes in the parent
        p.stdout.close()
# exit stack: wait for processes
if someprogram.returncode != 0: # errors shouldn't go unnoticed
   raise CalledProcessError(someprogram.returncode, someprogram.args)

注意:在我的Ubuntu机器上，尽管pass_fds自Python 3.2开始可用，但subprocess代码仅在Python 3.4+中有效.

Note: on my Ubuntu machine, the subprocess code works only in Python 3.4+, despite pass_fds being available since Python 3.2.

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