Interpolate variables into external programs call (subprocess.call/Popen) in Python - python

I'm trying to run an external program from a Python script.
After searching and reading multiple post here I came to what seemed to be the solution.
First, I used subprocess.call function.
If I build the command this way:
hmmer1=subprocess.call("D:\Python_Scripts\HMMer3\hmmsearch.exe --tblout hmmTestTab.out SDHA.hmm Test.fasta")
The external program D:\Python_Scripts\HMMer3\hmmsearch.exe is run taking hmmTestTab.out as file name for the output and SDHA.hmm and Test.fasta as input files.
Nevertheless, if I try to replace the file names with the variables outfile, hmmprofile and fastafile (I intend to receive those variables as arguments for the Python script and use them to build the external program call),
hmmer2=subprocess.call("D:\Python_Scripts\HMMer3\hmmsearch.exe --tblout outfile hmmprofile fastafile")
Python prints an error about being unable to open the input files.
I also used "Popen" function with analogous results:
This call works
hmmer3=Popen(['D:\Python_Scripts\HMMer3\hmmsearch.exe', '--tblout','hmmTestTab.out', 'SDHA.hmm','Test.fasta'])
and this one doesn't
hmmer4=Popen(['D:\Python_Scripts\HMMer3\hmmsearch.exe', '--tblout','outfile', 'hmmprofile','fastafile'])
As result of this, I presume I need to understand which is process to follow to interpolate the variables into the call, because it seems that the problem is there.
Would any of you help me with this issue?
Thanks in advance

You have:
hmmer4=Popen(['D:\Python_Scripts\HMMer3\hmmsearch.exe', '--tblout','outfile', 'hmmprofile','fastafile'])
But that's not passing the variable outfile. It's passing a string, 'outfile'.
You want:
hmmer4=Popen(['D:\Python_Scripts\HMMer3\hmmsearch.exe', '--tblout', outfile, hmmprofile, fastafile])
And the other answer is correct, though it addresses a different problem; you should double the backslashes, or use r'' raw strings.

Try to change this:
hmmer1=subprocess.call("D:\Python_Scripts\HMMer3\hmmsearch.exe"
to
hmmer1=subprocess.call('D:\\Python_Scripts\\HMMer3\\hmmsearch.exe'
Edit
argv = ' --tblout outfile hmmprofile fastafile' # your arguments
program = [r'"D:\\Python_Scripts\\HMMer3\\hmmsearch.exe"', argv]
subprocess.call(program)

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I have seen multiple posts on passing the string but not able to find good solution on reading the string passed to python script from batch file. Here is my problem.
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I have following in my python code.
import sys
passed_var = sys.argv[1]
When I run the above code I always see below error.
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Try this:
import sys
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If I have read your question and its formatting correctly, I think your .bat file should read:
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Or better still:
Set "string_var=123_Asdf"
"D:\BuildTools\tools\python27\python.exe" testscript.py "%string_var%"
Where %string_var% can be passed with or without its enclosing doublequotes.
Your batch file should be a bit simpler, make sure you have your PATH set correctly or else this won't work.
python testscript.py [argument]

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If your python script is just like that your function is never called and therefore doesn't return anything.
I don't know what kind of data you plan to return, if it's simple stuff the perhaps just print it with print(get_value(data)) in the end of the file and capture the printed lines with the VB script?

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I am trying to create a file that just writes the user's name to a file. I have written:
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In the console, using input function, you need to tell the program that you're sending him a string.
When it asks for the name, you shouldn't input for instance Bernard, but "Bernard".
You should use raw_input instead if you want to get rid of the " character.
PS : Have you tried running your program in the console using python command ? You would have seen the error message pop.
input is used to read integers.
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I am calling a Powershell script within a Python script using Python's subprocess Popen. The Powershell script requires two input parameters: -FilePath and -S3Key. It uploads a file to AWS S3 server. If I pass in hard coded strings, the script works.
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I know, it's an old question, so this is for those who find this question via google:
The solution mentioned in comment has some risks (string injection) and might not work if there are special characters involved. Better:
import subprocess
filename = r'C:\TEMP\test.txt'
uploadkey = 'mytrialtest/test.txt'
subprocess.Popen(['powershell',"-ExecutionPolicy","RemoteSig‌​ned","-File", './Upload.ps1', '-FilePath:', filename , '-S3Key:', uploadkey])
Notice the : appended to the parameter names - in most cases it will also work without the :, but if the value starts with a dash, it will fail without the :.

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datalist = open('tmp/lista.txt', 'r')
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Thanks in advance!
P.S.: I'm new to Python and fairly new to programming, so I apologise if this is due to a shallow understanding of a basic issue.
Where are the input file and where do you want to save the output file. For this kind of scripts i think that it's better use absolute paths
Use:
open('/tmp/lista.txt', 'r')
instead of:
open('tmp/lista.txt', 'r')
I think that the error can be related to this
It may have something to do with where you start your interpreter.
Try use a absolute path /tmp/randolista.txt instead of relative path tmp/randolista.txt to isolate the problem.

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