tabGcContent

#!/usr/bin/python

from sys import *
from optparse import OptionParser
import re, gzip

# === COMMAND LINE INTERFACE, OPTIONS AND HELP ===
parser = OptionParser("%prog [options] inFname field0Based - take a field as sequence from tab-sep file and show gc content as a new field ") 
#parser.add_option("", "--bestValueCutoff", dest="bestValueCutoff", action="store",  help="when determining the most parsimonous value, how much more support does the best value need from the second best value, default %default", default=2, type="int") 

def gcContent(seq):
    c = 0
    for x in seq:
        if x in ["G","C"]:
            c+= 1
    return int(round(100.0*(float(c)/len(seq))))
            

(options, args) = parser.parse_args()

if len(args)==0:
    parser.print_help()
    exit(0)

fname = args[0]
field = int(args[1])

for line in open(fname):
    fs = line.strip("\n").split()
    fs.append("%0d" % gcContent(fs[field]))
    print "\t".join(fs)