Run command line program from within Python

Question

I am trying to run a blat search from within my python code. Right now it's written as...

os.system('blat database.fa fastafile pslfile')

When I run the code, I specify file names for "fastafile" and "pslfile"...

python my_code.py -f new.fasta -p test.psl

This doesn't work as "fastafile" and "pslfile" are variables for files created and named when I run the code, but if I were to use the actual file names I would have to go back and change my code each time I run it. I'd like to use the command line arguments above to specify the files.

How would I change this so that "fastafile" and "pslfile" will be replaced with my arguments (new.fasta and test.psl) each time?

Answer 1

You should make use of argparse to take in command line arguments (it'll give you variables with names f and p that hold the file names), then just form the command string from there.

command_str = "blat database.fa " + f + " " + p
os.system(command_str)

https://docs.python.org/3.4/library/argparse.html#argparse.ArgumentParser.parse_args

ArgumentParser.parse_args(args=None, namespace=None)

Convert argument strings to objects and assign them as attributes of the namespace. Return the populated namespace.

Previous calls to add_argument() determine exactly what objects are created and how they are assigned. See the documentation for add_argument() for details.

By default, the argument strings are taken from sys.argv, and a new empty Namespace object is created for the attributes.

Answer 2

import os

fastaFile = sys.argv[1]
pslFile = sys.argv[2]

os.system("blat -f {0} -p {1}".format(fastaFile,pslFile))

#example run: python scriptName.py fasta.txt psl.txt

Answer 3

#!/usr/bin/env python2.7

from sys import argv

def main():
    if len(argv) != 3:
        print "usage: ./my_code.py -f *.fasta -p *.psl"
        raise SystemExit
    os.system('blat database.fa {} {}'.format(*argv[1:]))

if __name__ == '__main__':
    main()

Answer 4

Instead of using os.system , it's considered more pythonic to use subprocess.call , which eliminates the need to sanitize the input from argv:

subprocess.call(['blat', 'database.fa', '-f', 'new.fasta', '-p', 'test.psl'])

You can also incorporate ApolloFortyNine's answer and use Python's great argparse module to get the arguments and pass them onto subprocess.call .