概述

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？

#!/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)

另一种更优选的方法(不需要在磁盘上创建命名条目)来实现bash进程替换是使用/ dev / fd / N文件名(如果可用的话)为suggested by @Dunes.在FreeBSD上,fdescfs(5) (/dev/fd/#) creates entries for all file descriptors opened by the process.为了测试可用性,跑：

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

如果失败了;尝试将符号/ / dev / fd符号链接到proc(5),因为它在某些Linux上完成：

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

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

#!/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,子进程代码仅适用于Python 3.4,尽管自Python 3.2以来pass_fds可用.

总结

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