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Methylation_analysis.py
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#!/usr/bin/python
import sys
import re
f1 = open("../../Reapeat_analysis/FIMO/fimo_out/fimo.gff",'r')
f2 = open("3407_A_run459_ATGAGCAT_S9_L007_R1_001.fastq_bismark_pe.sam",'r')
f3 = open("../bigwig/1_CG_meth.bedgraph",'r')
f4 = open("../bigwig/1_CHG_meth.bedgraph",'r')
f5 = open("../bigwig/1_CHH_meth.bedgraph",'r')
f1.seek(0)
f2.seek(0)
f3.seek(0)
f4.seek(0)
f5.seek(0)
fOut = open("output_sample_x1.txt",'w')
for line1 in f1:
if not line1.startswith("#"):
line1 = line1.split('\t')
s1 = int(line1[3])
s2 = int(line1[4])
s0 = str(line1[0])
count = 0
percent = 0
lt = []
for line2 in f2:
line2 = line2.split("\t")
t1 = int(line2[3])
t2 = int(line2[3]) + 150
if (s0 == str(line2[2])):
if (t2 >= s1 >= t1):
percent = percent + ((t2-s1)/(s2-s1))*100
count = count + 1
if count >= 4:
try:
maxi = int(percent)/int(count)
except ZeroDivisionError:
maxi = 0
CG = []
for l3 in f3:
l3 = l3.split("\t")
if (s0 == str(l3[0])) and (s1 <= int(l3[1]) <= s2):
CG.append(float(l3[3]))
f3.seek(0)
try:
CG_M = sum(CG)/len(CG)
except ZeroDivisionError:
CG_M = 0
CHG = []
for l4 in f4:
l4 = l4.split("\t")
if (s0 == str(l4[0])) and (s1 <= int(l4[1]) <= s2):
CHG.append(float(l4[3]))
f4.seek(0)
try:
CHG_M = sum(CHG)/len(CHG)
except ZeroDivisionError:
CHG_M = 0
CHH = []
for l5 in f5:
l5 = l5.split("\t")
if (s0 == str(l5[0])) and (s1 <= int(l5[1]) <= s2):
CHH.append(float(l5[3]))
f5.seek(0)
try:
CHH_M = sum(CHH)/len(CHH)
except ZeroDivisionError:
CHH_M = 0
fOut.write(str(s1) +"\t"+ str(s2)+"\t"+ str(s0)+"\t"+ str(t1)+"\t"+ str(t2)+"\t"+ str(line2[2])+"\t"+str(count)+"\t"+str(maxi)+"\t"+str(CG_M)+"\t"+str(CHG_M)+"\t"+str(CHH_M)+"\n")
elif (t2 >= s2 >= t1):
percent = percent + ((s2-t1)/(s2-s1))*100
count = count + 1
if count >= 4:
try:
maxi = int(percent)/int(count)
except ZeroDivisionError:
maxi = 0
CG = []
for l3 in f3:
l3 = l3.split("\t")
if (s0 == str(l3[0])) and (s1 <= int(l3[1]) <= s2):
CG.append(float(l3[3]))
f3.seek(0)
try:
CG_M = sum(CG)/len(CG)
except ZeroDivisionError:
CG_M = 0
CHG = []
for l4 in f4:
l4 = l4.split("\t")
if (s0 == str(l4[0])) and (s1 <= int(l4[1]) <= s2):
CHG.append(float(l4[3]))
f4.seek(0)
try:
CHG_M = sum(CHG)/len(CHG)
except ZeroDivisionError:
CHG_M = 0
CHH = []
for l5 in f5:
l5 = l5.split("\t")
if (s0 == str(l5[0])) and (s1 <= int(l5[1]) <= s2):
CHH.append(float(l5[3]))
f5.seek(0)
try:
CHH_M = sum(CHH)/len(CHH)
except ZeroDivisionError:
CHH_M = 0
fOut.write(str(s1) +"\t"+ str(s2)+"\t"+ str(s0)+"\t"+ str(t1)+"\t"+ str(t2)+"\t"+ str(line2[2])+"\t"+str(count)+"\t"+str(maxi)+"\t"+str(CG_M)+"\t"+str(CHG_M)+"\t"+str(CHH_M)+"\n")
elif (t1 >= s1 and t2 <= s2):
percent = percent + ((t2-t1)/(s2-s1))*100
count = count + 1
if count >= 4:
try:
maxi = int(percent)/int(count)
except ZeroDivisionError:
maxi = 0
CG = []
for l3 in f3:
l3 = l3.split("\t")
if (s0 == str(l3[0])) and (s1 <= int(l3[1]) <= s2):
CG.append(float(l3[3]))
f3.seek(0)
try:
CG_M = sum(CG)/len(CG)
except ZeroDivisionError:
CG_M = 0
CHG = []
for l4 in f4:
l4 = l4.split("\t")
if (s0 == str(l4[0])) and (s1 <= int(l4[1]) <= s2):
CHG.append(float(l4[3]))
f4.seek(0)
try:
CHG_M = sum(CHG)/len(CHG)
except ZeroDivisionError:
CHG_M = 0
CHH = []
for l5 in f5:
l5 = l5.split("\t")
if (s0 == str(l5[0])) and (s1 <= int(l5[1]) <= s2):
CHH.append(float(l5[3]))
f5.seek(0)
try:
CHH_M = sum(CHH)/len(CHH)
except ZeroDivisionError:
CHH_M = 0
fOut.write(str(s1) +"\t"+ str(s2)+"\t"+ str(s0)+"\t"+ str(t1)+"\t"+ str(t2)+"\t"+ str(line2[2])+"\t"+str(count)+"\t"+str(maxi)+"\t"+str(CG_M)+"\t"+str(CHG_M)+"\t"+str(CHH_M)+"\n")
f2.seek(0)
fOut.close()
CHG.append(float(l4[3]))
f4.seek(0)
try:
CHG_M = sum(CHG)/len(CHG)
except ZeroDivisionError:
CHG_M = 0
CHH = []
for l5 in f5:
l5 = l5.split("\t")
if (s0 == str(l5[0])) and (s1 <= int(l5[1]) <= s2):
CHH.append(float(l5[3]))
f5.seek(0)
try:
CHH_M = sum(CHH)/len(CHH)
except ZeroDivisionError:
CHH_M = 0
fOut.write(str(s1) +"\t"+ str(s2)+"\t"+ str(s0)+"\t"+ str(t1)+"\t"+ str(t2)+"\t"+ str(line2[2])+"\t"+str(count)+"\t"+str(maxi)+"\t"+str(CG_M)+"\t"+str(CHG_M)+"\t"+str(CHH_M)+"\n")
elif (t1 >= s1 and t2 <= s2):
percent = percent + ((t2-t1)/(s2-s1))*100
count = count + 1
if count >= 4:
try:
maxi = int(percent)/int(count)
except ZeroDivisionError:
maxi = 0
CG = []
for l3 in f3:
l3 = l3.split("\t")
if (s0 == str(l3[0])) and (s1 <= int(l3[1]) <= s2):
CG.append(float(l3[3]))
f3.seek(0)
try:
CG_M = sum(CG)/len(CG)
except ZeroDivisionError:
CG_M = 0
CHG = []
for l4 in f4:
l4 = l4.split("\t")
if (s0 == str(l4[0])) and (s1 <= int(l4[1]) <= s2):
CHG.append(float(l4[3]))
f4.seek(0)
try:
CHG_M = sum(CHG)/len(CHG)
except ZeroDivisionError:
CHG_M = 0
CHH = []
for l5 in f5:
l5 = l5.split("\t")
if (s0 == str(l5[0])) and (s1 <= int(l5[1]) <= s2):
CHH.append(float(l5[3]))
f5.seek(0)
try:
CHH_M = sum(CHH)/len(CHH)
except ZeroDivisionError:
CHH_M = 0
fOut.write(str(s1) +"\t"+ str(s2)+"\t"+ str(s0)+"\t"+ str(t1)+"\t"+ str(t2)+"\t"+ str(line2[2])+"\t"+str(count)+"\t"+str(maxi)+"\t"+str(CG_M)+"\t"+str(CHG_M)+"\t"+str(CHH_M)+"\n")
f2.seek(0)
fOut.close()