python - 子进程中的多个管道

Question

我正在尝试在 ruffus 管道中使用 Sailfish，它将多个 fastq 文件作为参数。我在 python 中使用子进程模块执行 Sailfish，但是 <()即使我设置了 shell=True，子进程调用也不起作用.

这是我想使用 python 执行的命令:

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？子流程是正确的方法吗？

Answer 1

模拟bash process substitution :

#!/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:

#!/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()

哪里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法(无需在磁盘上创建命名条目)是使用 /dev/fd/N文件名(如果可用)为 suggested by @Dunes .在 FreeBSD 上， fdescfs(5) ( /dev/fd/# ) creates entries for all file descriptors opened by the process .要测试可用性，请运行:

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

如果失败；尝试符号链接(symbolic link) /dev/fd至 proc(5) 正如在某些 Linux 上所做的那样:

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

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

#!/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，subprocess代码仅适用于 Python 3.4+，尽管 pass_fds从 Python 3.2 开始可用。