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import argparse
import fileinput
def zero2one(input_vcf_file_name: str):
with fileinput.FileInput(input_vcf_file_name, inplace = True) as vcf_file:
for vcf_line in vcf_file:
if vcf_line[0] == "#":
print(vcf_line, end='')
continue
# From
#121_cassette_SSV9_CAG-eGFP-ISce-PASV40 3163 8622 A C . MULTIPLE Ty=SNP;Rk=8.0508e-05;UL=0;UR=0;CL=0;CR=0;Genome=A;Sd=1;XA=121_cassette_SSV9_CAG-eGFP-ISce-PASV40_17,121_cassette_SSV9_CAG-eGFP-ISce-PASV40_3081,121_cassette_SSV9_CAG-eGFP-ISce-PASV40_79 GT:DP:PL:AD:HQ ./.:2:.,.,.:2,0:0,0 0/0:291967:8727,869383,5824307:291691,276:71,48
# To
#121_cassette_SSV9_CAG-eGFP-ISce-PASV40 3163 8622 A C . MULTIPLE Ty=SNP;Rk=8.0508e-05;UL=0;UR=0;CL=0;CR=0;Genome=A;Sd=1;XA=121_cassette_SSV9_CAG-eGFP-ISce-PASV40_18,121_cassette_SSV9_CAG-eGFP-ISce-PASV40_3082,121_cassette_SSV9_CAG-eGFP-ISce-PASV40_80 GT:DP:PL:AD:HQ ./.:2:.,.,.:2,0:0,0 0/0:291967:8727,869383,5824307:291691,276:71,48
vcf_line = vcf_line.strip().split()
new_POS = int(vcf_line[1]) + 1
ID_REF_ALT_QUAL_FILTER = '\t'.join(vcf_line[2:7])
INFO = vcf_line[7]
# zero to one for XA positions
s_INFO = INFO.split(';')
if s_INFO[-1].startswith("XA="):
XA="XA="
all_XAs = s_INFO[-1].split("=")[-1].split(',')
for current_XA in all_XAs:
pos = int(current_XA.split("_")[-1]) + 1
XA += "_".join(current_XA.split("_")[:-1])+"_"+str(pos)+","
XA = XA[:-1] # remove additional ','
INFO = ';'.join(s_INFO[:-1]) + ";" + XA
end_line = '\t'.join(vcf_line[8:])
new_vcf_line = f"{vcf_line[0]}\t{new_POS}\t{ID_REF_ALT_QUAL_FILTER}\t{INFO}\t{end_line}"
print(new_vcf_line)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("-i", help="name of input zero-based vcf file (will be overwritten!)", dest='input_vcf_file', type=str, required=True)
args = parser.parse_args()
zero2one(args.input_vcf_file)
print(f"Transformed zero-based {args.input_vcf_file} to one-based")
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