A question about subprocess taking input from command line and returning output!

[Aurimas]

I am tryin to think of how to ask an input to be a text file. It can be any .pdb file like 1abc.pdb, 2abc.pdb, 3drt.pdb, etc.
I am working with upgrading the above script to this:

from subprocess import Popen, PIPE

file = raw_input("> ")
read_file = file.format
open_file = open('read_file', 'r+') 

cat = ['cat', 'open_file']
get = ['voronota', 'get-balls-from-atoms-file', '--annotated']
calc = ['voronota', 'calculate-contacts', '--annotated']
que = [
    'voronota', 'query-contacts', '--inter-residue',
    '--match-first', 'R<ARG>',
    '--match-second', 'c<solvent>']
awk = ['awk', '{sum += $3} END {print sum}']
 
cat = Popen(cat, stdout=PIPE)
get = Popen(get, stdin=cat.stdout, stdout=PIPE)
calc = Popen(calc, stdin=get.stdout, stdout=PIPE)
que = Popen(que, stdin=calc.stdout, stdout=PIPE)
awk = Popen(awk, stdin=que.stdout, stdout=PIPE, stderr=PIPE)
out, err = awk.communicate()
print(out)

but am getting this error:

Error:
Traceback (most recent call last):
  File "voronota_script.py", line 4, in <module>
    open_file = open('read_file', 'r+')
IOError: [Errno 2] No such file or directory: 'read_file'

How is it possible to ask an input to be a txt file (in my case x.pdb where x has 28 different values)?