base_number = 0
total_bases = 0
no_bases = 0
with gzip.open(directory + '/' + output) as genos:
for line in genos:
Data = line.decode().strip('\n') # Convert bytes into string
l = Data.split('\t')
sampleDepth = int(l[4])
n = int(l[2]) # sample number
total_bases += int(l[4])
p = []
if 1 in ploidy:
haploid = l[9:11]
haploid_sum = generics.log_or_zero(
sum(map(lambda x: generics.exp_or_zero(float(x)),
haploid)))
p.append(haploid_sum)
if 2 in ploidy:
diploid = l[11:14]
diploid_sum = generics.log_or_zero(
sum(map(lambda x: generics.exp_or_zero(float(x)),
diploid)))
p.append(diploid_sum)
if 3 in ploidy:
triploid = l[14:18]
triploid_sum = generics.log_or_zero(
sum(map(lambda x: generics.exp_or_zero(float(x)),
triploid)))
p.append(triploid_sum)
if 4 in ploidy:
index_of_X.append(index)
myReads.base=myReads.base.replace('X','')
#Remove all corresponding base qualities
count=0
for i in index_of_X:
myReads.base_quality = myReads.base_quality[:i-count] + myReads.base_quality[i+1-count:]
count+=1
#find sample depth of filtered data
sampleDepth = len(myReads.base)
p=[] # list to fill with probabilities for this base
if 1 in ploidy:
haploid = generics.calcGenoLogLike1_MajorMinor(myReads,mySite,major,minor)
haploid_sum = generics.log_or_zero(sum(map(lambda x,y: generics.exp_or_zero(x)*y,haploid,HWE_Prob_hap)))
p.append(haploid_sum)
if 2 in ploidy:
diploid = generics.calcGenoLogLike2_MajorMinor(myReads,mySite,major,minor)
diploid_sum = generics.log_or_zero(sum(map(lambda x,y: generics.exp_or_zero(x)*y,diploid,HWE_Prob_dip)))
p.append(diploid_sum)
if 3 in ploidy:
triploid = generics.calcGenoLogLike3_MajorMinor(myReads,mySite,major,minor)
triploid_sum = generics.log_or_zero(sum(map(lambda x,y: generics.exp_or_zero(x)*y,triploid,HWE_Prob_tri)))
p.append(triploid_sum)
if 4 in ploidy:
tetraploid = generics.calcGenoLogLike4_MajorMinor(myReads,mySite,major,minor)
tetraploid_sum = generics.log_or_zero(sum(map(lambda x,y: generics.exp_or_zero(x)*y,tetraploid,HWE_Prob_tetra)))
myReads = Reads(base, qualities)
#find sample depth of filtered data
sampleDepth = len(myReads.base)
if sampleDepth > args.max_x_meandepth * meandepths[
n - 1]:
sampleDepth = 0
myReads = Reads("", "")
p = [
] # list to fill with probabilities for this base
if 1 in ploidy:
haploid = generics.calcGenoLogLike1_MajorMinor(
myReads, mySite, major, minor)
haploid = list(
map(
lambda x, y: generics.log_or_zero(
generics.exp_or_zero(x) * y),
haploid, HWE_Prob_hap))
if 2 in ploidy:
diploid = generics.calcGenoLogLike2_MajorMinor(
myReads, mySite, major, minor)
diploid = list(
map(
lambda x, y: generics.log_or_zero(
generics.exp_or_zero(x) * y),
diploid, HWE_Prob_dip))
if 3 in ploidy:
triploid = generics.calcGenoLogLike3_MajorMinor(
myReads, mySite, major, minor)
triploid = list(
