Optparse Option Actions

I'm working with optparse, and I'm writing a script with 3 commandline arguments. The first one (-qtype) specifies whether information needs to be called from a local file, or from the web. Then depending on this, the 2nd argument (-qname) is either a string of nucleotides, or a FASTA filename. The 3rd argument (-output) is the output filename.

My question is if there is an optparse option action that I can use for the 1st argument (since the standard "store," "append," etc do not apply in this case).

Here is what I have so far: (it is likely laced with errors)

import optparse

if False:#__name__== '__main__':
    # parser object for managing input options
    parser = optparse.OptionParser()

    parser.add_option( '-qtype' ,  action = ‘?’ )
    parser.add_option( '-qname' , action = ‘?’ , […] )
    parser.add_option( '-output' , action = ‘store’ , type = ‘?’ , dest = ‘filename’ )

    # load the inputs
    args = [‘-qtype’ , ‘-qname’ , ‘-output’]
    (options , args) = parser.parse_args()

I have question marks and [...] where I am boggled over how to approach this problem.

Solution

Option 1: Use arguments instead of options

This might be a viable approach since it seems you might require all three inputs from the user to run normally.

According to the optparse docs

A program should be able to run just fine with no options whatsoever

In this case your solution would like

import optparse
import sys

if __name__ == '__main__':
    parser = optparse.OptionParser()

    (options, args) = parser.parse_args()

    if len(args) != 3:
        print 'please specify all required arguments - qtype qname output_file'
        sys.exit(-1)

    qtype, qname, output = args

    if qtype == 'web':
        pass
    elif qtype == 'local':
        pass
    else:
        print 'no qtype specified! exiting'
        sys.exit(-1)

Then you can use all the arguments as strings and either process them directly or turn them into files / url for web requests.

Example command line:

program.py  web  blah blah

Option 2: Use options anyway

import optparse
import sys

if __name__ == '__main__':
    parser = optparse.OptionParser()

    parser.add_option('--qtype', action='store', dest='qtype', type='string')
    parser.add_option('--qname', action='store', dest='qname', type='string')
    parser.add_option('--output', action='store', type='string', dest='filename')

    (options, args) = parser.parse_args()
    if options.qtype == 'web':
        pass
    elif options.qtype == 'local':
        pass
    else:
        print 'no qtype specified! exiting'
        sys.exit(-1)

Example usage:

program.py --qtype web --qname blah --output blah