Filtering One File by Another File

colfilter.py

#!/usr/bin/env python2.7

from argparse import ArgumentParser
import sys

def parseArg():
	'''parse command line arguments'''
	parser = ArgumentParser()
	parser.add_argument('-i', '--input', dest='input', metavar='INPUT',\
			type=file, default=sys.stdin, help='Full input file')
	parser.add_argument('-f', '--filter', dest='filter', metavar='OUTPUT',\
			type=file, help='File for filtering out sub lines of input file')
	parser.add_argument('-1', dest='col1', type=int, default=1,\
			metavar='NUM',\
			help='Column number for input file to match filter file')
	parser.add_argument('-2', dest='col2', type=int, default=1,\
			metavar='NUM',\
			help='Column number of filter file')
	parser.add_argument('-s', '--sep', dest='sep', type=str, default=None,\
			metavar='SEP',\
			help='Field seperater, default is whitespace character')
	return parser.parse_args()

def cacheFilter(filer, col=0, sep=None):
	'''read filter file for match'''
	filters = {}
	for line in filer:
		linelist = line.split(sep)
		filters[linelist[col]] = 1
	return filters

def main():
	'''main process'''
	opts = parseArg()
	opts.col1 -= 1
	opts.col2 -= 1
	if opts.col1 < 0 or opts.col2 < 0:
		raise SystemExit("Col must be greater than 0")
	filters = cacheFilter(opts.filter, opts.col2, opts.sep)
	for line in opts.input:
		llist = line.split(opts.sep)
		if llist[opts.col1] in filters:
			sys.stdout.write(line)
	sys.stdout.flush()

if __name__ == '__main__':
	main()