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docopt boolean arg python

Tags:

python

docopt

I use following args for my script with doctopt

Usage:
GaussianMixture.py --snpList=File --callingRAC=File

Options:
-h --help     Show help.
snpList     list snp txt
callingRAC      results snp

I would like to add an argument that have a conditional consequence on my script : correct my datas or don't correct my datas. Something like :

Usage:
GaussianMixture.py --snpList=File --callingRAC=File  correction(--0 | --1)

Options:
-h --help     Show help.
snpList     list snp txt
callingRAC      results snp
correction      0 : without correction | 1 : with correction 

And I would like to add in my script an if in some functions

def func1():
  if args[correction] == 0:
      datas = non_corrected_datas
  if args[correction] == 1:
      datas = corrected_datas

But I don't know how to write it in the usage neither in my script.

like image 726
Elysire Avatar asked Oct 25 '25 23:10

Elysire


1 Answers

EDIT: My original answer didn't take into account OP's requirements for --correction to be mandatory. Syntax was incorrect in my original answer. Here's a tested working example:

#!/usr/bin/env python
"""Usage:
    GaussianMixture.py --snpList=File --callingRAC=File --correction=<BOOL>

Options:
    -h, --help          Show this message and exit.
    -V, --version       Show the version and exit
    --snpList         list snp txt
    --callingRAC      results snp
    --correction=BOOL Perform correction?  True or False.  [default: True]

"""

__version__ = '0.0.1'

from docopt import docopt

def main(args):
    args = docopt(__doc__, version=__version__)
    print(args)

    if args['--correction'] == 'True':
        print("True")
    else:
        print("False")

if __name__ == '__main__':
    args = docopt(__doc__, version=__version__)
    main(args)

Please let me know if this works for you.

like image 138
Dustin Keib Avatar answered Oct 28 '25 13:10

Dustin Keib