将perl脚本应用于目录中的每个文件，并使用Python获取输出

Question

I am trying to make a python script that will open a directory, apply a perl script to every file in that directory and get its out put in either multiple text files or just one.

I currently have:

import shlex, subprocess
arg_str = "perl tilt.pl *.pdb > final.txt"
arg = shlex.split(arg_str)

import os
framespdb = os.listdir("prac_frames")

for frames in framespdb:
        subprocess.Popen(arg, stdout=True)

---

I keep getting *.pdb not found. I am very new to all of this so any help trying to complete this script would help.

Answer 1

*.pdb not found means exactly that - there won't be a *.pdb in whatever directory you're running the script... and as I read the code - I don't see anything to imply it's within 'frames' when it runs the perl script.

you probably need os.chdir(path) before the Popen. How do I "cd" in Python?

...using a python script to run somewhat dubious syscalls to perl may offend some people but everyone's done it.. aside from that I'd point out:

always specify full paths (this becomes a problem if you will later say, want to run your job automatically from cron or an environment that doesn't have your PATH). ie 'which perl' - put that full path in.

./ .pdb would be better but not as good as the fullpath/ .pdb (which you could use instead of the os.chdir option).

Answer 2

        subprocess.Popen(arg, stdout=True)

does not expand filename wildcards. To handle your *.pdb , use shell=True .