CODEWITHSUNDEEP
pythonsubprocesspastezcat
Fatemeh Ashari
Fatemeh Ashari

Reputation: 13

How to run paste <(zcat f1.gz) <(zcat f2.gz) using python's subprocess?

I am trying to run paste <(zcat f1.gz) <(zcat f2.gz) using subprocess. Here's what I have done so far:

ps1 = subprocess.Popen(('zcat', 'f1.gz'), stdout=subprocess.PIPE)
ps2 = subprocess.Popen(('zcat', 'f2.gz'), stdout=subprocess.PIPE)
ps3 = subprocess.Popen('paste', stdout=subprocess.PIPE, stdin=subprocess.PIPE)

But I am not sure how to provide ps3 with both ps1.stdout and ps2.stdout as inputs. I would appreciate it if you guys can help me with this and let me know if I am on the right track.

Upvotes: 1

Views: 134

Answers (1)

qouify
qouify

Reputation: 3900

My answer is largely inspired by this post allowing multiple inputs to python subprocess where the problem is slightly different.

Basically one solution is to use a fifo : subprocesses write in the fifo while a thread consumes data written by subprocesses.

import subprocess
import os
import threading

#  create our fifo for data exchange between processes
os.mkfifo('my-fifo')

#  create a reader thread that consumes data from our fifo
def read_from_fifo():
    with open('my-fifo', 'rb') as fd:
        subprocess.Popen('paste', stdin=fd)
t = threading.Thread(target=read_from_fifo) 
t.start()

#  write commands output to our fifo
with open('my-fifo', 'wb') as fifo:
    for cmd in [('zcat', 'f1.gz'), ('zcat', 'f2.gz')]:
        p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
        fifo.write(p.stdout.read())

t.join()  # wait that our thread has consumed all data
os.unlink('my-fifo')

Upvotes: 1

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