在 python 中找出管道

Question

我目前正在 python 中编写程序，但我被卡住了。所以我的问题是：我有一个程序可以读取文件并将一些行打印到标准输出，如下所示：

#imports
import sys

#number of args
numArgs = len(sys.argv)

#ERROR if not enough args were committed
if numArgs <= 1:
    sys.exit("Not enough arguments!")

#naming input file from args
Input = sys.argv[1]

#opening files
try:
    fastQ = open(Input , 'r')
except IOError, e:
    sys.exit(e)

#parsing through file
while 1:

    #saving the lines
    firstL = fastQ.readline()
    secondL = fastQ.readline()

    #you could maybe skip these  lines to save ram
    fastQ.readline()
    fastQ.readline()

    #make sure that there are no blank lines in the file
    if firstL == "" or  secondL == "":
        break

    #edit the Header to begin with '>'
    firstL = '>' + firstL.replace('@' , '')

    sys.stdout.write(firstL)
    sys.stdout.write(secondL)

#close both files
fastQ.close()

现在我想重写这个程序，这样我就可以运行一个像这样的命令行：zcat "textfile" | python "myprogram" > "otherfile"。所以我环顾四周，发现了子流程，但似乎无法弄清楚该怎么做。感谢您的帮助

编辑：

Now, if what you are doing is trying to write a Python script to orchestrate the execution of both zcat and myprogram, THEN you may need subprocess. – rchang

打算将 "textfile" 和程序放在集群上，因此我不需要从集群复制任何文件。我只想登录集群并使用 command:zcat "textfile" | python "myprogram" > "otherfile"，以便 zcat 和程序执行它们的操作，我最终在集群上得到 "otherfile"。希望你明白我想做什么。

编辑#2：

我的解决方案

#imports
import sys
import fileinput

# Counter, maybe there is a better way
count = 0

# Iterieration over Input
for line in fileinput.input():

    # Selection of Header
    if count == 0 :

        #Format the Header
        newL = '>' + line.replace('@' , '')

        # Print the Header without newline
        sys.stdout.write(newL)

    # Selection of Sequence
    elif count == 1 :

        # Print the Sequence
        sys.stdout.write(line)

    # Up's the Counter
    count += 1
    count = count % 4

谢谢

Answer 1

您可以使用 fastQ = sys.stdin 从标准输入而不是文件读取输入，或者（更一般地）fastQ = fileinput.input() 从命令行指定的标准输入 and/or 文件读取。

还有fileinput.hook_compressed这样就不需要zcat直接读取压缩文件了：

$ myprogram textfile >otherfile

在 python 中找出管道

Figuring out pipes in python

bash

python-2.7

pipe

subprocess