Python25

#!/usr/bin/env python

import os
import sys
import math

in1=sys.argv[1]
in2=sys.argv[2]
ou1=sys.argv[3]

u=open(ou1,'w')

genelist=[]
with open(in2,'r') as y:
    yi=y.readlines()
    for yil in yi:
        yili=yil.strip().split('\n')
        genelist.append(str(yili[0]))

geneconlist=[]
with open(in1,'r') as s:
    si=s.readlines()
    for sil in si[1:]:
        sili=sil.strip().split('\t')
        genename=str(sili[1])
        if genename in genelist:
            if genename not in geneconlist:
                geneconlist.append(genename)
                num1=math.log10(float((float(sili[2])+float(sili[3])+float(sili[4]))/3))
                num2=math.log10(float((float(sili[5])+float(sili[6])+float(sili[7]))/3))
                num3=math.log10(float((float(sili[8])+float(sili[9])+float(sili[10]))/3))
                u.write(str(sili[1])+'\t'+str(num1)+'\t'+str(num2)+'\t'+str(num3)+'\n')