1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
|
#!/bin/python
# -*- coding: utf-8 -*-
###################################
#Transforms a 1-based vcf into 0-based vcf
# usage : one2zeroBased_vcf.py vcf_file
import sys
from functionsVCF_creator import *
file=open(sys.argv[1],"r")
VCFfile=open("VCFone2zeroBAsed.vcf","w")
for line in file:
if "#" == line[0]:
print((line,))
continue
line=line.rstrip('\n')
#SNP_higher_path_3 117 3 C G . . Ty=SNP;Rk=1.00000;UL=86;UR=261;CL=.;CR=.;C1=124,0;C2=0,134 GT:DP:PL 0/0:124:10,378,2484 1/1:134:2684,408,10
splitted_line = line.split("\t")
# decrease the position value if it is a number:
if str.isdigit(splitted_line[1].strip()):
splitted_line[1]=int(splitted_line[1])#-1
# prints the line
printOneline(splitted_line,VCFfile)
|
