如何从第二个脚本中执行包含argparse的脚本

Question

I have this simple script named test1.py .

#!/usr/bin/env python

from argparse import ArgumentParser


def cmdlineparse():
    parser = ArgumentParser()
    parser.add_argument("-tid", dest="CHEMBL_TARGET_ID", required=True, type=str)
    parser.add_argument("-molfile", dest="XTEST_MOLFILE", required=False, type=str)

    args=parser.parse_args()
    return args


if __name__ == '__main__':

    args = cmdlineparse()

    print("The given CHEMBL_TARGET_ID is %s" % args.CHEMBL_TARGET_ID)
    print("The given XTEST_MOLFILE is %s" % args.XTEST_MOLFILE)

Normally, I execute it like this ./test1.py -tid CHEMBL8868 -molfile ligands.sdf .

What I want to do is to execute it multiple times from within a second script named test2.py . The simplest solution would be to call it using subprocess.call or something equivalent.

subprocess.call("./test1.py -tid CHEMBL8868 -molfile ligands.sdf".split(), shell=True, executable='/bin/bash')

However, I would like to do it in a more elegant way, namely by importing it as a module and passing values to argparse . Could someone please show me how to do this?

Answer 1

You'll need to refactor your script a bit: let cmdlineparse take an list of arguments to parse, and define a function main that does the actual work instead of a bare block guarded by __main__ .

#!/usr/bin/env python

from argparse import ArgumentParser


def cmdlineparse(args):
    parser = ArgumentParser()
    parser.add_argument("-tid", dest="CHEMBL_TARGET_ID", required=True, type=str)
    parser.add_argument("-molfile", dest="XTEST_MOLFILE", required=False, type=str)

    args=parser.parse_args(args)
    return args

def main(args=None):
    args = cmdlineparse(args)
    print("The given CHEMBL_TARGET_ID is %s" % args.CHEMBL_TARGET_ID)
    print("The given XTEST_MOLFILE is %s" % args.XTEST_MOLFILE)


if __name__ == '__main__':
    main()

Without an argument, main will parse the current command-line arguments, since a value of None passed (eventually) to parser.parse_args() will cause it to parse sys.argv[1:] .

Now you can import test1 and call main explicitly as often as you like:

import test1

test1.main(["-tid", "CHEMBL8868", "-molfile", "ligands.sdf"])
test1.main(["-tid", "CHEMBL8293", "-molfile", "stuff.sdf"])
# etc