Problem Passing Arguement to do loop

[stephenmolnar]

Had to make some changes to your changes:

#!/usr/bin/env python2.5
# -*- coding: utf-8 -*-
import subprocess
import sys
with open('ligands') as infile:
ligand = infile.read().strip().split()
for nvar in ligand:
command = [
"./pythonsh", "./prepare_ligand4.py",
"-l", nvar + ".mol2",
"-o", nvar + ".pbdqt" ]
proc = subprocess.Popen(command, stdout=subprocess.PIPE)
out, err = proc.communicate()
print(out)
print(err)
if proc.returncode:
print ('Subprocess FAILED:', proc.command)

Here are the results:

runfile('/sdc1/Apps/Modeling/FileEditing/untitled1m2.py', wdir='/sdc1/Apps/Modeling/FileEditing')
Traceback (most recent call last):

File "/home/comp/Apps/miniconda3/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3296, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)

File "<ipython-input-1-51b00a34bbcd>", line 1, in <module>
runfile('/sdc1/Apps/Modeling/FileEditing/untitled1m2.py', wdir='/sdc1/Apps/Modeling/FileEditing')

File "/home/comp/Apps/miniconda3/lib/python3.7/site-packages/spyder_kernels/customize/spydercustomize.py", line 824, in runfile
execfile(filename, namespace)

File "/home/comp/Apps/miniconda3/lib/python3.7/site-packages/spyder_kernels/customize/spydercustomize.py", line 110, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)

File "/sdc1/Apps/Modeling/FileEditing/untitled1m2.py", line 17
print 'Subprocess FAILED:', proc.command
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('Subprocess FAILED:', proc.command)?




runfile('/sdc1/Apps/Modeling/FileEditing/untitled1m2.py', wdir='/sdc1/Apps/Modeling/FileEditing')
Traceback (most recent call last):

File "/home/comp/Apps/miniconda3/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3296, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)

File "<ipython-input-2-51b00a34bbcd>", line 1, in <module>
runfile('/sdc1/Apps/Modeling/FileEditing/untitled1m2.py', wdir='/sdc1/Apps/Modeling/FileEditing')

File "/home/comp/Apps/miniconda3/lib/python3.7/site-packages/spyder_kernels/customize/spydercustomize.py", line 824, in runfile
execfile(filename, namespace)

File "/home/comp/Apps/miniconda3/lib/python3.7/site-packages/spyder_kernels/customize/spydercustomize.py", line 110, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)

File "/sdc1/Apps/Modeling/FileEditing/untitled1m2.py", line 12
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stdout=subprocess.PIPE)
^
SyntaxError: keyword argument repeated




runfile('/sdc1/Apps/Modeling/FileEditing/untitled1m2.py', wdir='/sdc1/Apps/Modeling/FileEditing')
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