Question

我正在尝试使用Sailfish，它在ruffus管道中使用多个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<()，子进程调用中的shell=True也不起作用。

这是我想用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

模仿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()

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优选的方法（不需要在磁盘上创建命名条目）是使用/dev/fd/N文件名（如果它们可用）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;尝试将/dev/fd符号链接到proc(5)，因为它已在某些Linux上完成：

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

这是基于/dev/fd的{{1}} bash命令的实现：

someprogram <(someprocess) <(anotherprocess)

注意：在我的Ubuntu机器上，#!/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)代码仅适用于Python 3.4+，尽管自Python 3.2以来subprocess可用。

Answer 2

虽然J.F. Sebastian使用命名管道提供了答案，但可以使用匿名管道来完成此操作。

import shlex
from subprocess import Popen, PIPE

inputcmd0 = "zcat hello.gz" # gzipped file containing "hello"
inputcmd1 = "zcat world.gz" # gzipped file containing "world"

def get_filename(file_):
    return "/dev/fd/{}".format(file_.fileno())

def get_stdout_fds(*processes):
    return tuple(p.stdout.fileno() for p in processes)

# setup producer processes
inputproc0 = Popen(shlex.split(inputcmd0), stdout=PIPE)
inputproc1 = Popen(shlex.split(inputcmd1), stdout=PIPE)

# setup consumer process
# pass input processes pipes by "filename" eg. /dev/fd/5
cmd = "cat {file0} {file1}".format(file0=get_filename(inputproc0.stdout), 
    file1=get_filename(inputproc1.stdout))
print("command is:", cmd)
# pass_fds argument tells Popen to let the child process inherit the pipe's fds
someprogram = Popen(shlex.split(cmd), stdout=PIPE, 
    pass_fds=get_stdout_fds(inputproc0, inputproc1))

output, error = someprogram.communicate()

for p in [inputproc0, inputproc1, someprogram]:
    p.wait()

assert output == b"hello\nworld\n"

子流程中的多个管道

2 个答案: