script.py

#!/usr/bin/python

import sys

fname = sys.argv[-1]

codon_to_aa = {}
codon_to_aa["gct"] = "A"
codon_to_aa["gcc"] = "A"
codon_to_aa["gca"] = "A"
codon_to_aa["gcg"] = "A"
codon_to_aa["cgt"] = "R"
codon_to_aa["cgc"] = "R"
codon_to_aa["cga"] = "R"
codon_to_aa["cgg"] = "R"
codon_to_aa["aga"] = "R"
codon_to_aa["agg"] = "R"
codon_to_aa["aat"] = "N"
codon_to_aa["aac"] = "N"
codon_to_aa["gat"] = "D"
codon_to_aa["gac"] = "D"
codon_to_aa["tgt"] = "C"
codon_to_aa["tgc"] = "C"
codon_to_aa["caa"] = "Q"
codon_to_aa["cag"] = "Q"
codon_to_aa["gaa"] = "E"
codon_to_aa["gag"] = "E"
codon_to_aa["ggt"] = "G"
codon_to_aa["ggc"] = "G"
codon_to_aa["gga"] = "G"
codon_to_aa["ggg"] = "G"
codon_to_aa["cat"] = "H"
codon_to_aa["cac"] = "H"
codon_to_aa["att"] = "I"
codon_to_aa["atc"] = "I"
codon_to_aa["ata"] = "I"
codon_to_aa["atg"] = "M"
codon_to_aa["tta"] = "L"
codon_to_aa["ttg"] = "L"
codon_to_aa["ctt"] = "L"
codon_to_aa["ctc"] = "L"
codon_to_aa["cta"] = "L"
codon_to_aa["ctg"] = "L"
codon_to_aa["aaa"] = "K"
codon_to_aa["aag"] = "K"
codon_to_aa["ttt"] = "F"
codon_to_aa["ttc"] = "F"
codon_to_aa["cct"] = "P"
codon_to_aa["ccc"] = "P"
codon_to_aa["cca"] = "P"
codon_to_aa["ccg"] = "P"
codon_to_aa["tct"] = "S"
codon_to_aa["tcc"] = "S"
codon_to_aa["tca"] = "S"
codon_to_aa["tcg"] = "S"
codon_to_aa["agt"] = "S"
codon_to_aa["agc"] = "S"
codon_to_aa["act"] = "T"
codon_to_aa["acc"] = "T"
codon_to_aa["aca"] = "T"
codon_to_aa["acg"] = "T"
codon_to_aa["tgg"] = "W"
codon_to_aa["tat"] = "Y"
codon_to_aa["tac"] = "Y"
codon_to_aa["gtt"] = "V"
codon_to_aa["gtc"] = "V"
codon_to_aa["gta"] = "V"
codon_to_aa["gtg"] = "V"
codon_to_aa["taa"] = "*"
codon_to_aa["tga"] = "*"
codon_to_aa["tag"] = "*"

linestring = open(fname, "r")

for line in linestring:
  line.split()[1]	
	if linearr[0].isupper:
		linearr[0] = x

print x_linestring.find("D"+"E"+"C"+"H")