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import sys
import gzip
if len(sys.argv)<2:
print ("This tool removes from discoSnp sorted VCF the locus which are tri-allelic or more")
print ("python3 remove_non_diploids.py \".vcf from discoSnp\" ")
sys.exit()
if "gz" in sys.argv[1]:
coherent_file=gzip.open(sys.argv[1],"r")
else:
coherent_file=open(sys.argv[1],"r")
previous_line=""
previous_chr=""
previous_pos=""
previous_triploid=False
while True:
line = coherent_file.readline().rstrip()
if not line: break
if line[0]=='#':
print (line)
continue
# SNP_higher_path_3 196 3 C G . . Ty=SNP;Rk=1;UL=86;UR=261;CL=166;CR=761;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/0:124:10,378,2484:124,0:0,0 1/1:134:2684,408,10:0,134:0,0
splitted_line = line.split()
chr=splitted_line[0]
pos=splitted_line[1]
if chr==previous_chr and pos==previous_pos:
previous_triploid=True
continue
else:
if not previous_triploid and len(previous_line)>0:
print (previous_line)
previous_chr=chr
previous_pos=pos
previous_triploid=False
previous_line=line
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