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debreak_merge.py
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debreak_merge.py
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import time
import os
import pysam
import denovo_static
import sys
def mergerpossort(a):
return int(a.split('\t')[1])
def mergerlensort(a):
return int(a.split('\t')[2])
def m_samechr_insertion(samechrom):
ins=[]
samechrom.sort(key=mergerpossort)
samechrom+=['last_end\t999999999999\t999999999999\t1\t60\t0']
candi=[]
last=samechrom[0]
for event in samechrom:
maxlen=max(int(event.split('\t')[2]),int(last.split('\t')[2]))
window=max(300,maxlen+10)
window=min(800,window)
if int(event.split('\t')[1]) < int(last.split('\t')[1])+window :
candi+=[event]
last=sorted(candi,key=mergerlensort)[-1]
continue
if len(candi)==1:
ins+=[candi[0]]
else:
position=0; length=0; count=0; quality=0; sd=0; readnames=''
candi.sort(key=mergerlensort,reverse=True)
for can in candi:
if int(can.split('\t')[2])>=0.5*length:
can_count=int(can.split('\t')[3])
position=int((position*count+int(can.split('\t')[1])*can_count)/(count+can_count))
length=int((length*count+int(can.split('\t')[2])*can_count)/(count+can_count))
quality=(quality*count+float(can.split('\t')[4])*can_count)/(count+can_count)
sd=(sd*count+float(can.split('\t')[5])*can_count)/(count+can_count)
readnames+=can.split('\t')[6]+';'
count+=can_count
readnames=readnames[:-1]
ins+=[candi[0].split('\t')[0]+'\t'+str(position)+'\t'+str(length)+'\t'+str(count)+'\t'+str(quality)+'\t'+str(sd)+'\t'+readnames+'\tUnique']
candi=[event]
last=event
return ins
def sort_mostspupport(a):
return [int(a.split('\t')[3]),int(a.split('\t')[2])]
def m_samechr_deletion(samechrom):
dels=[]
samechrom.sort(key=mergerpossort)
samechrom+=['last_end\t999999999999\t999999999999\t1\t60\t0']
candi=[]
last=samechrom[0]
for event in samechrom:
maxlen=max(int(event.split('\t')[2]),int(last.split('\t')[2]))
window=max(300,maxlen+10)
window=min(800,window)
if int(event.split('\t')[1]) < int(last.split('\t')[1])+int(last.split('\t')[2])+200 and int(event.split('\t')[1])-int(last.split('\t')[1]) < window:
candi+=[event]
last=event
continue
if len(candi)==1:
dels+=[candi[0]]
else:
position=0; length=0; count=0; quality=0; sd=0; readnames=''
candi.sort(key=sort_mostspupport,reverse=True)
for can in candi:
if int(can.split('\t')[2])>=0.5*length:
can_count=int(can.split('\t')[3])
position=int((position*count+int(can.split('\t')[1])*can_count)/(count+can_count))
length=int((length*count+int(can.split('\t')[2])*can_count)/(count+can_count))
quality=(quality*count+float(can.split('\t')[4])*can_count)/(count+can_count)
sd=(sd*count+float(can.split('\t')[5])*can_count)/(count+can_count)
readnames+=can.split('\t')[6]+';'
count+=can_count
readnames=readnames[:-1]
dels+=[candi[0].split('\t')[0]+'\t'+str(position)+'\t'+str(length)+'\t'+str(count)+'\t'+str(quality)+'\t'+str(sd)+'\t'+readnames+'\tUnique']
candi=[event]
last=event
return dels
def mergertra(a):
return [a.split('\t')[2],int(a.split('\t')[3])]
def m_samechr_translocation(samechrom):
samechrom.sort(key=mergertra)
iftrue=0
while iftrue==0:
iftrue=1
for i in range(len(samechrom)-1):
if samechrom[i].split('\t')[2]==samechrom[i+1].split('\t')[2] and abs(int(samechrom[i].split('\t')[3])-int(samechrom[i+1].split('\t')[3]))<=800:
iftrue=0
if samechrom[i].split('\t')[0]==samechrom[i+1].split('\t')[0] and abs(int(samechrom[i].split('\t')[1])-int(samechrom[i+1].split('\t')[1]))<=1000:
count1=int(samechrom[i].split('\t')[4]); count2=int(samechrom[i+1].split('\t')[4])
pos1=(int(samechrom[i].split('\t')[1])*count1+int(samechrom[i+1].split('\t')[1])*count2)//(count1+count2)
pos2=(int(samechrom[i].split('\t')[3])*count1+int(samechrom[i+1].split('\t')[3])*count2)//(count1+count2)
quality=(float(samechrom[i].split('\t')[5])*count1+float(samechrom[i+1].split('\t')[5])*count2)/(count1+count2)
sd1=(float(samechrom[i].split('\t')[6])*count1+float(samechrom[i+1].split('\t')[6])*count2)/(count1+count2)
sd2=(float(samechrom[i].split('\t')[7])*count1+float(samechrom[i+1].split('\t')[7])*count2)/(count1+count2)
readname=samechrom[i].split('\t')[8]+';'+samechrom[i+1].split('\t')[8]
mergedtra=samechrom[i].split('\t')[0]+'\t'+str(pos1)+'\t'+samechrom[i].split('\t')[2]+'\t'+str(pos2)+'\t'+str(count1+count2)+'\t'+str(quality)+'\t'+str(sd1)+'\t'+str(sd2)+'\t'+readname+'\tTranslocation'
samechrom=samechrom[:i]+[mergedtra]+samechrom[i+2:]
else:
count1=int(samechrom[i].split('\t')[4]); count2=int(samechrom[i+1].split('\t')[4])
if count1>=count2:
samechrom.remove(samechrom[i+1])
else:
samechrom.remove(samechrom[i])
break
return samechrom
def standerd_varition(length):
avelen=sum(length)/float(len(length))
s=0.0
for c in length:
s+=(c-avelen)**2/float(len(length))
s=s**0.5
return s
def mergeinfosecpos(a):
return int(a.split('\t')[3])
def mergeinfo_translocation(candi,min_support):
chrom=candi[0].split('\t')[0]
secchr=[c.split('\t')[2] for c in candi]
secchr=max(set(secchr),key=secchr.count)
candi=[c for c in candi if c.split('\t')[2]==secchr]
candi.sort(key=mergeinfosecpos)
if len(candi)%2==0:
median=(int(candi[len(candi)//2-1].split('\t')[3])+int(candi[len(candi)//2].split('\t')[3]))//2
else:
median=int(candi[len(candi)//2].split('\t')[3])
candi=[ c for c in candi if abs(int(c.split('\t')[3])-median)<=800]
if len(candi)>=min_support:
pos1=[int(c.split('\t')[1]) for c in candi]
pos2=[int(c.split('\t')[3]) for c in candi]
qual=[float(c.split('\t')[4]) for c in candi]
sd1=standerd_varition(pos1)
sd2=standerd_varition(pos2)
readnames=''
for c in candi:
readnames+=c.split('\t')[5]+';'
readnames=readnames[:-1]
return [chrom+'\t'+str(sum(pos1)//len(pos1))+'\t'+secchr+'\t'+str(sum(pos2)//len(pos2))+'\t'+str(len(candi))+'\t'+str(sum(qual)/len(qual))+'\t'+str(sd1)+'\t'+str(sd2)+'\t'+readnames+'\tTranslocation']
else:
return []
def assign_candi_insertion(candi,mean1,mean2):
group1=[]
group2=[]
for c in candi:
if abs(int(c.split('\t')[2])-mean1)<=abs(mean2-int(c.split('\t')[2])):
group1+=[c]
else:
group2+=[c]
mean1_new=int(sum([int(c.split('\t')[2]) for c in group1])/len(group1))
mean2_new=int(sum([int(c.split('\t')[2]) for c in group2])/len(group2))
return [group1,group2,mean1_new,mean2_new]
def mergeinfolengthsort(a):
return int(a.split('\t')[2])
def mergeinfo_insertion(candi,min_support):
candi.sort(key=mergeinfolengthsort)
if len(candi)>=1.5*min_support:
upper=int(candi[len(candi)*3//4].split('\t')[2])
lower=int(candi[len(candi)//4].split('\t')[2])
if upper>3*lower:
svgroups=assign_candi_insertion(candi,upper,lower)
svgroups=assign_candi_insertion(candi,svgroups[2],svgroups[3])
svgroups=assign_candi_insertion(candi,svgroups[2],svgroups[3])
mergedsv=[]
if len(svgroups[0])>=min_support:
mergedsv+=mergeinfo_insertion_oneevent(svgroups[0],min_support)
if len(svgroups[1])>=min_support:
mergedsv+=mergeinfo_insertion_oneevent(svgroups[1],min_support)
if len(mergedsv)==2:
#mergedsv=[c+'\tCompoundSV' for c in mergedsv]
# Test for rescue FP
if int(mergedsv[0].split('\t')[3])>=int(mergedsv[1].split('\t')[3]):
mergedsv=[mergedsv[0]+'\tCompoundSV']
else:
mergedsv=[mergedsv[1]+'\tCompoundSV']
if len(mergedsv)==1:
mergedsv=[mergedsv[0]+'\tUnique']
return mergedsv
mergedsv=mergeinfo_insertion_oneevent(candi,min_support)
if len(mergedsv)==1:
return [mergedsv[0]+'\tUnique']
else:
return []
def mergeinfo_insertion_oneevent(candi,min_support):
candi.sort(key=mergeinfolengthsort)
while len(candi)>min_support-2:
if int(candi[-1].split('\t')[2]) > 1.5* int(candi[len(candi)//2].split('\t')[2]):
candi.remove(candi[-1])
continue
if int(candi[len(candi)//2].split('\t')[2]) > 1.5*int(candi[0].split('\t')[2]):
candi.remove(candi[0])
continue
break
if len(candi)>=min_support:
chrom=candi[0].split('\t')[0]
position=[int(c.split('\t')[1]) for c in candi]
length=[int(c.split('\t')[2]) for c in candi]
quality=[float(c.split('\t')[3]) for c in candi]
position=sum(position)//len(position)
quality=sum(quality)/float(len(quality))
stand=standerd_varition(length)
length=sum(length)//len(length)
readnames=''
for c in candi:
readnames+=c.split('\t')[4]+';'
readnames=readnames[:-1]
return[chrom+'\t'+str(position)+'\t'+str(length)+'\t'+str(len(candi))+'\t'+str(quality)+'\t'+str(stand)+'\t'+readnames]
else:
return []
def counttimesort_tra(a):
return [int(a.split('\t')[1]),int(a.split('\t')[3])]
def counttime_translocation(samechrom,min_support):
samechrom.sort(key=counttimesort_tra)
samechrtra=[]
start=int(samechrom[0].split('\t')[1])
candi=[]
window=800
for event in samechrom:
if int(event.split('\t')[1])<=start+window:
candi+=[event]
continue
if len(candi)>=min_support:
samechrtra+=mergeinfo_translocation(candi,min_support)
candi=[event]
start=int(event.split('\t')[1])
if len(candi)>=min_support:
samechrtra+=mergeinfo_translocation(candi,min_support)
candi=[]
return samechrtra
def counttimesort(a):
return [int(a.split('\t')[1]),int(a.split('\t')[2])]
def counttime_insertion(samechrom,min_support):
if samechrom==[]:
return []
samechrom.sort(key=counttimesort)
samechrins=[]
start=int(samechrom[0].split('\t')[1])
candi=[]
inslength=[]
window=100
for event in samechrom:
if int(event.split('\t')[1])<=start+window:
candi+=[event]
inslength+=[int(event.split('\t')[2])]
continue
if window==100:
length=sum(inslength)//len(inslength)
if length<=100:
window=200
if 100<length<=500:
window=400
if length>500:
window=800
if int(event.split('\t')[1])<=start+window:
candi+=[event]
inslength+=[int(event.split('\t')[2])]
continue
if len(candi)>=min_support:
samechrins+=mergeinfo_insertion(candi,min_support)
candi=[event]
inslength=[int(event.split('\t')[2])]
start=int(event.split('\t')[1])
window=100
if len(candi)>=min_support:
samechrins+=mergeinfo_insertion(candi,min_support)
candi=[]
return samechrins
def counttime_deletion(samechrom,min_support):
if samechrom==[]:
return []
samechrom.sort(key=counttimesort)
samechrdel=[]
start=int(samechrom[0].split('\t')[1])
candi=[]
dellength=[]
window=100
for event in samechrom:
if int(event.split('\t')[1])<=start+window:
candi+=[event]
dellength+=[int(event.split('\t')[2])]
continue
if window==100:
length=sum(dellength)//len(dellength)
if length<=100:
window=200
if 100<length<=500:
window=400
if length>500:
window=800
if int(event.split('\t')[1])<=start+window:
candi+=[event]
dellength+=[int(event.split('\t')[2])]
continue
if len(candi)>=min_support:
samechrdel+=mergeinfo_insertion(candi,min_support)
candi=[event]
dellength=[int(event.split('\t')[2])]
start=int(event.split('\t')[1])
window=100
if len(candi)>=min_support:
samechrdel+=mergeinfo_insertion(candi,min_support)
candi=[]
return samechrdel
def merge_deletion(min_support,min_quality,readpath,samechrom_deletion,chrom,svtype,upper_bound):
delt1=time.time()
samechrom_deletion=[c for c in samechrom_deletion if float(c.split('\t')[3])>=min_quality]
if samechrom_deletion==[]:
return True
tt1=time.time()
deletions=counttime_deletion(samechrom_deletion,min_support)
deletions=[c for c in deletions if int(c.split('\t')[3])>=min_support]
f=open(readpath+svtype+'-info-'+chrom,'w')
for d in deletions:
f.write(d+'\n')
f.close()
real=[c for c in deletions if c.split('\t')[-1]=='Unique']
comp=[c for c in deletions if c.split('\t')[-1]=='CompoundSV']
cleaneddels=m_samechr_deletion(real)
cleaneddels+=comp
cleaneddels.sort(key=counttimesort)
if upper_bound:
cleaneddels=[c for c in cleaneddels if min_support<=int(c.split('\t')[3])<=min_support*30]
else:
cleaneddels=[c for c in cleaneddels if min_support<=int(c.split('\t')[3])]
f=open(readpath+svtype+'-merged-'+chrom,'w')
if svtype=='del':
sv_type='Deletion'
if svtype=='dup':
sv_type='Duplication'
if svtype=='inv':
sv_type='Inversion'
merged_result=[]
for d in cleaneddels:
f.write(d+'\t'+sv_type+'\n')
merged_result+=[d+'\t'+sv_type]
f.close()
delt2=time.time()
return merged_result
def merge_insertion(min_support,min_quality,readpath,samechrom_insertion,chrom,svtype,upper_bound):
samechrom_insertion=[c for c in samechrom_insertion if float(c.split('\t')[3])>=min_quality]
if samechrom_insertion==[]:
return True
inst1=time.time()
insertions=counttime_insertion(samechrom_insertion,min_support)
f=open(readpath+svtype+'-info-'+chrom,'w')
for d in insertions:
f.write(d+'\n')
f.close()
real=[c for c in insertions if c.split('\t')[-1]=='Unique']
compound=[c for c in insertions if c.split('\t')[-1]=='CompoundSV']
cleanedins=m_samechr_insertion(real)
cleanedins+=compound
cleanedins.sort(key=counttimesort)
if upper_bound:
cleanedins=[c for c in cleanedins if min_support<=int(c.split('\t')[3])<=30*min_support]
else:
cleanedins=[c for c in cleanedins if min_support<=int(c.split('\t')[3])]
f=open(readpath+svtype+'-merged-'+chrom,'w')
if svtype=='ins':
sv_type='Insertion'
if svtype=='inv':
sv_type='Inversion'
merged_result=[]
for d in cleanedins:
f.write(d+'\t'+sv_type+'\n')
merged_result+=[d+'\t'+sv_type]
f.close()
inst2=time.time()
return merged_result
def finalsorttra(a):
return [a.split('\t')[0],int(a.split('\t')[1])]
def merge_translocation(min_support,min_qual,readpath,samechrom_translocation,chrom,upper_bound):
samechrom_translocation=[c for c in samechrom_translocation if float(c.split('\t')[4])>=min_qual]
if samechrom_translocation==[]:
return True
trat1=time.time()
translocations=counttime_translocation(samechrom_translocation,min_support)
translocations=m_samechr_translocation(translocations)
if upper_bound:
translocations=[c for c in translocations if int(c.split('\t')[4])<=30*min_support]
translocations.sort(key=finalsorttra)
merged_result=[]
f=open(readpath+'tra-merged-'+chrom,'w')
for d in translocations:
f.write(d+'\n')
merged_result+=[d]
f.close()
trat2=time.time()
return merged_result
def genotype(depth,outpath):
highcov=depth*2
allae=open(outpath+'assembly_errors.bed','r').read().split('\n')[:-1]
samfile=pysam.AlignmentFile(outpath+'read_to_contig.bam',"rb")
f=open(outpath+'assembly_errors.bed-gt_test','w')
coll=0
expan=0
inv=0
for c in allae:
chrom=c.split('\t')[0]
start=int(c.split('\t')[1])
stop=int(c.split('\t')[2])
#print (c)
if start<0:
continue
if 'Expansion' in c or 'Inversion' in c:
leftcov=samfile.count(chrom,max(start-100,0),start,read_callback='all')
rightcov=samfile.count(chrom,stop,stop+100,read_callback='all')
#if leftcov>highcov and rightcov>highcov:
# continue
if 'Collapse' in c:
leftcov=samfile.count(chrom,max(0,start-100),start,read_callback='all')
rightcov=samfile.count(chrom,stop,stop+100,read_callback='all')
# if leftcov>highcov and rightcov>highcov:
# continue
if 'Expan' in c:
expan+=1
if 'Coll' in c:
coll+=1
if 'Inv' in c:
inv+=1
gtinfo='./.'
if int(c.split('\t')[3])>=0.6*min(leftcov,rightcov):
gtinfo='1/1'
else:
gtinfo='1/0'
#f.write(c+'\t'+gtinfo+'\n')
f.write(c+'\t'+gtinfo+'\t'+str(leftcov)+'\t'+str(rightcov)+'\t'+str(min(rightcov,leftcov))+'\n')
f.close()
'''
f=open(outpath+'summary_statistics','a')
f.write('After Genotyping:\n')
f.write('Number of assembly collapse\t'+str(coll)+'\n')
f.write('Number of assembly expansion\t'+str(expan)+'\n')
f.write('Number of assembly inversion\t'+str(inv)+'\n\n\n')
'''
'''
f.write('Number of assembly collapse in large contigs\t'+str(coll_large)+'\n')
f.write('Number of assembly expansion in large contigs\t'+str(expan_large)+'\n')
f.write('Number of assembly inversion in large contigs\t'+str(inv_large)+'\n\n\n')
'''
f.close()
return True