Redirect stdin to devnull, to avoid a subprocess to pause waiting for user input:
import os
from subprocess import Popen
try:
from subprocess import DEVNULL # Python 3
except ImportError:
DEVNULL = open(os.devnull, 'r+b', 0)
Popen(['pdflatex', 'file.tex'], stdin=DEVNULL, stdout=DEVNULL, stderr=DEVNULL)
I assume that you don't care about stdout/stderr also.