Question

I’m trying to write a script that asks for an input file and then runs some command on it. when I run the script it askes me for filename and when I give the file (e.g example.bam) then I get this error:

NameError: name ‘example.bam’ is not defined

I tried many things but I couldn’t fix it. Can someone tell me what is wrong?

This is my comand:

from subprocess import call
filename = input ("filename: ");
with open (filename, "r") as a:
    for command in ("samtools tview 'a' /chicken/chick_build2.1_unmasked.fa",):
        call(command, shell=True)

This is a short version of my command: it has to do much more stuff. I’m also thinking to input 4-6 files at same time (perhaps this information is helpful to clarify my intentions).

Answer 1

input is equivalent to eval(raw_input(prompt)). So what your script currently tries to do is interpret your input (“example”, in your case), and execute as if it were a statement in your script. For user input (and might I simply say “for any input” — unless you know what you’re doing), always use the raw_input function.

So, to solve it, replace input with raw_input:

filename = raw_input("filename: ")