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

[Aurimas]

Dear Python forum members,

The script I have written below (the_script.py) works fine with this terminal command at MAC OS Mojave Python 2.7:

python the_script.py < ABC.pdb > ABC.txt

! However I want my script (the_script.py below) written through terminal to be like this:

python the_script.py ABC.pdb

!
And not involve < or > and return the output to ABC.txt. The .pdb file is a text file as well.

#!/usr/bin/python2

import sys

import subprocess

process = subprocess.Popen(
		["voronota","get-balls-from-atoms-file","--annotated"],stdin=subprocess.PIPE,
		stdout=subprocess.PIPE)

output=process.communicate(sys.stdin.read())[0];

print output

I will look forward to all the replies.

Sincerely,
Aurimas

[Gribouillis]

Replace sys.stdin.read() with pathlib.Path('ABC.pdb').read_text() and replace print(output) with pathlib.Path('ABC.txt').write_text(output). Use the argparse module to get the file names from the command line.

The script I have written below

In 2019, use python 3.

[DeaD_EyE]

Don't forget that the built-in print function has a file keyword where to output the text.
In the case where a line has no line-ending/line-seperator, you could use the print funciton.
It adds by default a newline to the end of the string. This could be controlled with the keyword end

In [1]: print?                                                                  
Docstring:
print(value, ..., sep=' ', end='\n', file=sys.stdout, flush=False)

Prints the values to a stream, or to sys.stdout by default.
Optional keyword arguments:
file:  a file-like object (stream); defaults to the current sys.stdout.
sep:   string inserted between values, default a space.
end:   string appended after the last value, default a newline.
flush: whether to forcibly flush the stream.
Type:      builtin_function_or_method

[Aurimas]

Thank you guys, but I want to specify what pdb file I choose to use (like 1abc.pdb, 1fgh.pdb or other) and the output I need is

awk '{sum += $3} END {print sum}'

that prints a numerical value to terminal. Full terminal command in linux/mac would be

cat HS_1abc.pdb | voronota get-balls-from-atoms-file --annotated | voronota calculate-contacts --annotated | voronota query-contacts --inter-residue --match-first 'R<ARG>' --match-second 'c<solvent>' | awk '{sum += $3} END {print sum}'

I also need the program to say what R in --match-second to use (in this case it is ARG but it can have any one of 20 different values). Also for --match-second I need to define up to fours values like c<A,B,C,D>, c<A,B), c<W,C>, c<solvent>, c<A,C,E> or other letters

How could that be possible with pipes and subprocess and communicate?

[Gribouillis]

I would try something like this

from subprocess import Popen, PIPE

cat = ['cat', 'HS_1abc.pdb']
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)

[Aurimas]

Thank you. Should the code be run through python3? I have python 2.7 :(
My main struggle is to make an input being asked before running the script as in your given example I give an input as a string which would require me to write hundreds of different .pdb codes. I would like the script to ask first and then give the numerical value. Otherwise I am better doing it through terminal which I am doing now. Perhaps I need to include dictionary where I could run the calculations :-)

[Gribouillis]

I have python 2.7 :(

It is a matter of a few seconds to install a better python.

[Aurimas]

Installed Python3 but it works with 2.7 as well. How I could write in terminal: python script 1abc.pdb press enter and get:
XXXXXX - the sum of third columns values
With the written code I get the sum but have to change script all the time to get the correct value, which is wasteful as I have a lot of arguments to change (in ten hundreds or more) :/
Also how I could make 8 line of your proposed code to ask the input for 'R<AAA>' where the script asks to enter AAA as ARG, ASN, ASP, GLN, GLY or any other amino acid three digit code.

[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)?