39 lines
1.1 KiB
Python
39 lines
1.1 KiB
Python
|
import sys
|
||
|
|
genotype_vcf = open(sys.argv[1])
|
||
|
|
sites_vcf = open(sys.argv[2],'w')
|
||
|
|
|
||
|
|
sample_name = "ALL_HET"
|
||
|
|
info = "."
|
||
|
|
format = "GT"
|
||
|
|
het = "0/1"
|
||
|
|
use_fields = range(7)
|
||
|
|
|
||
|
|
line_counter = 0
|
||
|
|
print("Reading genotype file...")
|
||
|
|
for line in genotype_vcf.readlines():
|
||
|
|
line_counter += 1
|
||
|
|
if ( line.startswith("#") and not line.startswith("#CHR") ):
|
||
|
|
sites_vcf.write(line)
|
||
|
|
elif ( line.startswith("#CHR") ):
|
||
|
|
sites_vcf.write("##source=vcfGenotypeToSites\n")
|
||
|
|
spline = line.strip().split("\t")
|
||
|
|
newfields = list()
|
||
|
|
for i in range(9):
|
||
|
|
newfields.append(spline[i])
|
||
|
|
newfields.append(sample_name)
|
||
|
|
sites_vcf.write("\t".join(newfields)+"\n")
|
||
|
|
else:
|
||
|
|
spline = line.strip().split("\t")
|
||
|
|
newfields = list()
|
||
|
|
for i in use_fields:
|
||
|
|
newfields.append(spline[i])
|
||
|
|
newfields.append(info)
|
||
|
|
newfields.append(format)
|
||
|
|
newfields.append(het)
|
||
|
|
sites_vcf.write("\t".join(newfields)+"\n")
|
||
|
|
if ( line_counter % 100000 == 0 ):
|
||
|
|
print("Converted: "+str(line_counter)+" lines")
|
||
|
|
|
||
|
|
genotype_vcf.close()
|
||
|
|
sites_vcf.close()
|