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#!/usr/bin/env python
# -*- coding: utf-8 -*-
''' ***********************************************
Script to select only one variant per locus (cluster) in a discoSnp vcf output file (.vcf)
Author - Claire Lemaitre, Pierre Peterlongo, Inria
Usage:
python3 1SNP_per_cluster.py -i vcf_file [-o new_vcf_file]
Details:
The selected variant is not chosen at random, for a given cluster, it is the one with the less missing genotypes (if ties, it is the first read in the input file)
*********************************************** '''
import sys
import getopt
def usage():
'''Usage'''
print("-----------------------------------------------------------------------------")
print(sys.argv[0]+" : selects one variant per cluster")
print("-----------------------------------------------------------------------------")
print("usage: "+sys.argv[0]+" -i vcf_file [-o output_file]")
print(" -i: vcf file [mandatory]")
print(" -o: output vcf file (default = stdout)")
print(" -h: help")
print("-----------------------------------------------------------------------------")
sys.exit(2)
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "hi:o:")
except getopt.GetoptError as err:
# print help information and exit:
print(str(err))
usage()
sys.exit(2)
# Default parameters
vcf_file = None
out_file = None
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
sys.exit()
elif opt in ("-i"):
vcf_file = arg
elif opt in ("-o", "--out"):
out_file = arg
else:
assert False, "unhandled option"
if vcf_file==None:
print ("Error: option -i is mandatory")
usage()
sys.exit(2)
format_ok = check_format(vcf_file)
if not format_ok:
print("Error: the format of the input vcf is not correct, it must contain clustering information")
sys.exit(2)
dict_, nb_SNP_before, nb_SNP_after = store_info(vcf_file)
output_newvcf(vcf_file, out_file, dict_)
def check_format(vcf_file):
''' Checks if the vcf has the correct format, ie : the INFO field must contain clustering information, such as:
Ty=SNP;Rk=1;UL=1;UR=2;CL=.;CR=.;Genome=.;Sd=.;Cluster=79466;ClSize=12
'''
filin = open(vcf_file, 'r')
checked = False
while not checked:
line = filin.readline()
if line.startswith("#"): continue
INFO_split = line.split("\t")[7].split(";")
checked = True
if len(INFO_split) < 10: return False
tmp_cluster = INFO_split[8].split("Cluster=")
if len(tmp_cluster) < 2: return False
if tmp_cluster[1] == ".": return False
try:
cl_id = int(tmp_cluster[1])
except ValueError:
return False
return True
filin.close()
def store_info(vcf_file):
dict_ = {} ## {num_cluster : [num_SNP ayant le moins de géno manquants, nb_missgeno]}
filin = open(vcf_file, 'r')
nb_SNP_tot = 0
while True:
"""#SNP_higher_path_14643 30 14643 C T . . Ty=SNP;Rk=0.55424;UL=0;UR=0;CL=0;CR=0;Genome=.;Sd=.;Cluster=1285;ClSize=4 GT:DP:PL:AD:HQ 0/1:38:554,48,75:7,31:71,71 0/1:20:63,23,263:15,5:71,71"""
line = filin.readline()
if not line: break
if line.startswith("#"): continue
nb_SNP_tot += 1
num_cluster = int(line.split("Cluster=")[1].split(";")[0])
if num_cluster == -1: continue
id_SNP = line.split("\t")[2]
if num_cluster not in dict_:
dict_[num_cluster] = ["x", sys.maxsize] # ghost best variant for this new cluster
genotypes = [i.split(":")[0] for i in line.split("\t")[9:]]
nb_missing = 0
for ind in genotypes:
if ind[0] == "." :
nb_missing += 1
if nb_missing >= dict_[num_cluster][1]: continue
dict_[num_cluster] = [id_SNP, nb_missing]
filin.close()
return dict_, nb_SNP_tot, len(dict_)
def output_newvcf(vcf_file, out_file, dict_) :
filin = open(vcf_file, 'r')
if out_file:
filout=open(out_file,'w')
else:
filout = sys.stdout
while True:
line = filin.readline() #SNP_higher_path_14643 30 14643 C T . . Ty=SNP;Rk=0.55424;UL=0;UR=0;CL=0;CR=0;Genome=.;Sd=.;Cluster=1285;ClSize=4 GT:DP:PL:AD:HQ 0/1:38:554,48,75:7,31:71,71 0/1:20:63,23,263:15,5:71,71
if not line: break
if line.startswith("#"):
filout.write(line)
continue
try:
cluster = int(line.split("Cluster=")[1].split(";")[0])
except ValueError:
print ("No cluster size information stored in the vcf, exit")
sys.exit(1)
if cluster == -1 : continue
id_SNP = line.split("\t")[2]
if id_SNP != dict_[cluster][0]: continue
filout.write(line)
filin.close()
filout.close()
if __name__ == "__main__":
main()
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