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Copy pathRemove_clustered_variants.py
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Remove_clustered_variants.py
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"""
Combine Cluster filter wth other filters
"""
import os, sys, gzip, datetime
def main(chrom):
cluster = "/gpfs/group/stsi/data/projects/wellderly/GenomeComb/clustered_variants/clustered." + chrom + ".vcf.gz"
infile = "/gpfs/group/stsi/data/projects/wellderly/GenomeComb/vcf_filtered_VQHIGH_whiteOnly/wellderly_inova.VQHIGH.0.95white."+chrom+".vcf.gz"
outputfile = "/gpfs/group/stsi/data/projects/wellderly/GenomeComb/vcf_filtered_VQHIGH_whiteOnly_clustered/wellderly_inova.VQHIGH.0.95white.nocluster."+chrom+".vcf.gz"
counter_file = "/gpfs/group/stsi/data/projects/wellderly/GenomeComb/vcf_filtered_VQHIGH_whiteOnly_clustered/cluster_filters_counter.txt"
counterf = open(counter_file, 'a')
cl = gzip.open(cluster)
input_file = gzip.open(infile)
o = gzip.open(outputfile, 'w')
#counterf.write("\t\t\tWellderly\t\t\tInova\n")
#counterf.write("AF\tTotal Var\t Filtered Var\t<0.01\t0.01-0.05\t>0.05\t<0.01\t0.01-0.05\t>0.05\n")
cluster_dict = dict()
#PUT the cluster file in a dictionary
for line in cl:
if "#" in line:
continue
#keep only the entries with yes
elif "YES" in line:
tp_line = line.split("\t")
key = tp_line[1] + "_" + tp_line[3] + "_" + tp_line[4]
cluster_dict[key] = "YES"
file_buffer = ""
counter = 0
counter_unique_no_pass = 0
good_lines = 0
well_001 = 0
well_005 = 0
well_005_plus = 0
inova_001 = 0
inova_005 = 0
inova_005_plus = 0
for line in input_file:
counter = counter + 1
if line[:1] == "#":
#o.write(line)
continue
else:
tp_line = line.split("\t")
key = tp_line[1] + "_" + tp_line[3] + "_" + tp_line[4]
try:
if cluster_dict[key]:
counter_unique_no_pass = counter_unique_no_pass + 1
alleles = tp_line[4].split(",")
total_well_alleles = 0
total_inova_alleles = 0
total_well_alt = 0
total_inova_alt = 0
dict_of_alleles_well={}
dict_of_alleles_inova={}
well_AF = 0
inova_AF = 0
if len(alleles) > 1:
#print "len alleles > 1"
#create a dictionary that would count the number of alleles
for index, i in enumerate(alleles):
#add one to the index, alleles start at 1
ind = index + 1
dict_of_alleles_well[ind] = 0
dict_of_alleles_inova[ind] = 0
for index, gen in enumerate(tp_line[9:]):
index = index + 9
if len(alleles) == 1:
#tp_gen = gen[:3]
#First Allele
if gen[0] == "0":
if index < 529:
total_well_alleles += 1
else:
total_inova_alleles += 1
elif gen[0] == "1":
if index < 529:
total_well_alleles += 1
total_well_alt +=1
else:
total_inova_alleles += 1
total_inova_alt +=1
#Second Allele
if gen[2] == "0":
if index < 529:
total_well_alleles += 1
else:
total_inova_alleles += 1
elif gen[2] == "1":
if index < 529:
total_well_alleles += 1
total_well_alt +=1
else:
total_inova_alleles += 1
total_inova_alt +=1
else:
#print "Multi alleles"
#First Allele
if gen[0] != ".":
if gen[0] == "0":
if index < 529:
total_well_alleles += 1
else:
total_inova_alleles += 1
else:
if index < 529:
total_well_alleles += 1
#Increment the dictionary value for that allele
try:
dict_of_alleles_well[int(gen[0])] +=1
except:
print "gen[0] " + str(gen[0])
print "alleles " + tp_line[4]
else:
total_inova_alleles += 1
try:
dict_of_alleles_inova[int(gen[0])] +=1
except:
print "gen[0] " + str(gen[0])
print "alleles " + tp_line[4]
#Second Allele
if gen[2] != ".":
if gen[2] == "0":
if index < 529:
total_well_alleles += 1
else:
total_inova_alleles += 1
else:
if index < 529:
total_well_alleles += 1
#Increment the dictionary value for that allele
try:
dict_of_alleles_well[int(gen[2])] +=1
except:
print "gen[0] " + str(gen[2])
print "alleles " + tp_line[4]
else:
total_inova_alleles += 1
try:
dict_of_alleles_inova[int(gen[2])] +=1
except:
print "gen[0] " + str(gen[2])
print "alleles " + tp_line[4]
inova_max_value = max(dict_of_alleles_inova.values())
well_max_value = max(dict_of_alleles_well.values())
try:
if len(alleles) == 1:
well_AF = float(total_well_alt)/float(total_well_alleles)
else:
# For multi allelic values remove the highest AF from 1
well_AF = 1 - float(well_max_value)/float(total_well_alleles)
#print str(AF)
except:
well_AF = 0.0
try:
if len(alleles) == 1:
inova_AF = float(total_inova_alt)/float(total_inova_alleles)
else:
inova_AF = 1 - float(inova_max_value)/float(total_inova_alleles)
#print str(AF)
except:
inova_AF = 0.0
if well_AF < 0.01:
well_001 += 1
elif well_AF < 0.05:
well_005 += 1
else:
well_005_plus += 1
if inova_AF < 0.01:
inova_001 += 1
elif inova_AF < 0.05:
inova_005 += 1
else:
inova_005_plus +=1
except:
good_lines = good_lines + 1
file_buffer = file_buffer + line
if counter%100 == 0:
o.write(file_buffer)
file_buffer = ""
o.flush()
if counter%10000 ==0:
print "Total lines"
print str(counter)
print "No pass lines"
print str(counter_unique_no_pass)
sys.stdout.flush()
o.write(file_buffer)
file_buffer = ""
o.flush()
print "Total lines"
print str(counter)
print "New Filtered out lines"
print str(counter_unique_no_pass)
print "Good lines "
print str(good_lines)
AF_counter = chrom + "\t" + str(counter) + "\t" + str(counter_unique_no_pass) + "\t" + str(well_001) + "\t" + str(well_005) + "\t" + str(well_005_plus) + \
"\t" + str(inova_001) + "\t" + str(inova_005) + "\t" + str(inova_005_plus) + "\n"
print AF_counter
counterf.write(AF_counter)
counterf.close()
o.close()
cl.close()
input_file.close()
if __name__ == '__main__':
print "Python Version: " + sys.version
#args = parse_args()
#import time
#start = time.time()
main(sys.argv[1])
#main(sys.argv[1], sys.argv[2], sys.argv[3])
#end = time.time()
#print 'This took {0} seconds'.format(end - start)