getopts in python

[bio_informatics]

I am new to python, have been working in perl. I am trying to implement getopts in python, but I am failing to understand it.


I have the below code:

#!/usr/bin/python

from Bio import SeqIO
import sys, getopt

def main(argv):
   
   for i in argv:
    print "This is in for loop "+i
   
   listfile = ''
   pdbfile = ''
   
   try:
      opts, args = getopt.getopt(argv,"pdb:list:",["pfile=","lfile="])
   except getopt.GetoptError:
      print 'check.py -pdb <pdbfile> -list <listfile>'
      
      sys.exit(2)
   for opt, arg in opts:
      
      if opt in ("-pdb","--pfile"):
         pdbfile = arg
         
      if opt in ("-list","--lfile"):
         listfile = arg
   print 'Input file is "', listfile
   print 'Output file is "', pdbfile

if __name__ == "__main__":
   main(sys.argv[1:])

I run it as:
./check.py -pdb ~/Documents/pdb/pdb_seqres.txt -list ~/Documents/pdb/list.txt
The output I get is:

This is in for loop -pdb
This is in for loop /home/sariya/Documents/pdb/pdb_seqres.txt
This is in for loop -list
This is in for loop /home/sariya/Documents/pdb/list.txt
Input file is "
Output file is "

when I print arg, I get blank. so it tells me there is not value passed in arg. Why?

So my pdbfile and listfile are getting blank.
Please guide.

[blancha]

You may have your reasons to prefer using the getopts module, but I really like the argparse module, especially in Python 3.4.

Very simple, intuitive and powerful.

https://docs.python.org/3.4/library/argparse.html#module-argparse

[R.W.W.Brouwer]

In the Python getopts module, short arguments are a single character by default.

so
> opts, args = getopt.getopt(argv,"pdb:list:",["pfile=","lfile="])

should be:
> opts, args = getopt.getopt(argv,"p:l:",["pfile=","lfile="])

And your assignment should be then become:

> if opt in ("-p","--pfile"):
and
> if opt in ("-l","--lfile"):

The drawback of using argparse is that this module is not standard in Python 2.6.

[bio_informatics]

@R.W.W.Brouwer - Thank you for pointing out the issue. I didn't know about single character.

@blancha - I didn't know for argparse. I will try that too.