import sys
import os
chro_order=['shit']
for i in range(1,24):
        chro_order.append('chr'+str(i))
chro_order.append('chrX')
chro_order.append('chrY')
chro_order.append('chrM')
fn=sys.argv[1]
dfh=open(fn,'r')
rfh=open(fn.split('/')[-1][:-4]+'_mod.txt','w')
sample1=fn.replace('L2_3','L23').split('_')
sample=sample1[5]+'_'+'_'.join(sample1[:5])
rfh.write('000000000000000000000000_Sample\t'+sample+'\n')
for i in dfh:
        line=i.split()
	if line[0] in chro_order and line[3] in chro_order and line[0]==line[3] and line[1]!=line!=[4]:
		if chro_order.index(line[0])>=10:
			index1=str(chro_order.index(line[0])*10000000000+int(line[1]))
		if chro_order.index(line[0])<10:
			index1='0'+str(chro_order.index(line[0])*10000000000+int(line[1]))
		if chro_order.index(line[3])>=10:
			index2=str(chro_order.index(line[3])*10000000000+int(line[4]))
		if chro_order.index(line[3])<10:
			index2='0'+str(chro_order.index(line[3])*10000000000+int(line[4]))
		index=index1+index2
		rfh.write(index+'_'+'_'.join(line[0:6])+'\t'+line[6]+'\n')
rfh.close()
#os.system('sort -k 1b,1 '+fn.split('/')[-1][:-4]+'_mod_temp.txt > '+fn.split('/')[-1][:-4]+'_mod.txt')
##os.system('rm '+fn.split('/')[-1]+'_CpG_mod_temp.txt')