vcf2hap.py

Author: zhangrui2018@picb.ac.cn

vcf2hap.py

@@ -0,0 +1,71 @@
+import argparse
+from numpy import *
+
+def vcf2hap(input, chr, output):
+	f = open(input+".vcf", 'r')
+	g1 = open(output+".hap", 'w')	
+	g2 = open(output+".ind", 'w')
+	g3 = open(output+".pos", 'w')
+
+	A = []
+	if chr != 'X':
+		for a in f:
+			if a[0] == "#" and a[1] == "C":
+				a = a.split()
+				for i in range(9, len(a)):
+					g2.write(a[i]+"\n")
+			elif a[0] != "#":
+				a = a.split()
+				g3.write(a[1]+"\t"+a[3]+"\t"+a[4]+"\n")
+				A1 = []
+				for i in range(9, len(a)):
+					A1.append(a[i][0])
+					A1.append(a[i][2])
+				A.append(A1)
+	else:
+		for a in f:
+			if a[0] == "#" and a[1] == "C":
+				a = a.split()
+				for i in range(9, len(a)):
+					g2.write(a[i]+"\n")
+			elif a[0] != "#":
+				a = a.split()
+				g3.write(a[1]+"\t"+a[3]+"\t"+a[4]+"\n")
+				A1 = []
+				for i in range(9, len(a)):
+					A1.append(a[i][0])
+					A1.append('9')
+				A.append(A1)
+
+	AM = mat(A)
+	AM = AM.T
+
+
+	for i in range(0, AM.shape[0]):
+		for j in range(0, AM.shape[1]):
+			g1.write(str(AM[i,j]))
+		g1.write("\n")
+
+	print("Done")
+
+	f.close()
+	g1.close()
+	g2.close()
+	g3.close()
+
+if __name__ == '__main__':
+	parser = argparse.ArgumentParser()
+	parser.add_argument("--input", type = str, required = True, \
+						help = "Prefix of input vcf")
+	parser.add_argument("--chr", type = str, required = True, \
+						help = "chromosome label, 1,2,...,22,X")
+	parser.add_argument("--output", type = str, required = True, \
+						help = "Prefix of output file(.hap, .ind, .pos)")
+
+	args = parser.parse_args()
+	if args.chr not in ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X']:
+		print("Error: not correct chr!")
+		exit()
+
+	vcf2hap(args.input, args.chr, args.output)
+