gistfile1.py

#!/usr/bin/env python

import os
from collections import defaultdict


def parseColors(colors):
    """
    Parse read id color specification.

    @param colors: A C{list}, each of whose elements is a C{str} such as
        'green id1 id2', where each of id1, id2 etc. is either a read
        identifier or the name of a file containing read identifiers one
        per line.
    @return: A C{dict} whose keys are colors and whose values are sets of
        read identifiers.
    """
    result = defaultdict(set)
    for colorInfo in colors:
        readIds = colorInfo.split()
        color = readIds.pop(0)
        for readId in readIds:
            if os.path.isfile(readId):
                with open(readId, 'r') as fp:
                    for line in fp:
                        result[color].add(line.rstrip())
            else:
                result[color].add(readId)
    return result

import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--color', action='append')
args = parser.parse_args()

for color, ids in parseColors(args.color).iteritems():
    print '%s: %s' % (color, ids)