getopt not quite working, what am I doing wrong?

Question

I am not sure why the code below does not work - I get the error

NameError: name 'group1' is not defined.

The code worked fine before I tried to use getopt.. I am trying to parse the command line input so that eg if I put

python -q file1 file2 -r file3 file4

the file1 and file2 become the input into my first loop as 'group1'.

import sys
import csv
import vcf
import getopt
#set up the args
try:
    opts, args = getopt.getopt(sys.argv[1:], 'q:r:h', ['query', 'reference', 'help'])
except getopt.GetoptError as err:
    print str(err)
    sys.exit(2)

for opt, arg in opts:
    if opt in ('-h', '--help'):
        print "Usage python -q [query files] -r [reference files]"
        print "-h this help message"
    elif opt in ('-q', '--query'):
        group1 = arg
    elif opt in ('-r', '--reference'):
        group2 = arg
    else:
        print"check your args"

#extract core snps from query file, saving these to the set universal_snps
snps = []
outfile = sys.argv[1]
for variants in group1:

    vcf_reader = vcf.Reader(open(variants))

Answer 1

The problem is that group1 = arg is never running, so when it later gets to for variants in group1:, the variable is not defined.

This is because you are calling the function incorrectly for how you defined your options. When you have the line:

 opts, args = getopt.getopt(sys.argv[1:], 'q:r:h', ['query', 'reference', 'help'])

There is a requirement that the arguments with flags (i.e. -q file1 and -r file3 be specified before any other arguments. Therefore, if you were to call the function as:

python <scriptName> -q file1 -r file3 file2 file4

You would have the intended behaviour. This is because all the parameters without an associated flag appear at the end of the call (and would be retrievable through the args parameter