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debreak_merge_cluster.py
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import os
import time
import sys
def mergeinfolengthsort(a):
return int(a.split('\t')[2])
def mergeinfo_insertion(candi,min_support,svtypeinfo):
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>1.75*lower and upper-lower>50:
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\t'+svtypeinfo for c in mergedsv]
if len(mergedsv)==1:
mergedsv=[mergedsv[0]+'\tUnique\t'+svtypeinfo]
return mergedsv
mergedsv=mergeinfo_insertion_oneevent(candi,min_support)
if len(mergedsv)==1:
return [mergedsv[0]+'\tUnique\t'+svtypeinfo]
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=sum([int(c.split('\t')[2]) for c in group1])//len(group1)
mean2_new=sum([int(c.split('\t')[2]) for c in group2])//len(group2)
return [group1,group2,mean1_new,mean2_new]
def mergeinfo_insertion_oneevent(candi,min_support):
candi.sort(key=mergeinfolengthsort)
while len(candi)>max(2,min_support-2):
if int(candi[-1].split('\t')[2]) > 2* int(candi[len(candi)//2].split('\t')[2]) and int(candi[-1].split('\t')[2]) -int(candi[len(candi)//2].split('\t')[2]) >30:
candi.remove(candi[-1])
continue
if int(candi[len(candi)//2].split('\t')[2]) > 2*int(candi[0].split('\t')[2]) and int(candi[len(candi)//2].split('\t')[2]) -int(candi[0].split('\t')[2]) >30:
candi.remove(candi[0])
continue
break
if len(candi)>=max(2,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')[6]) for c in candi]
position=sum(position)//len(position)
quality=sum(quality)//float(len(quality))
length=sum(length)//len(length)
readnames=''
for c in candi:
readnames+=c.split('\t')[4]+';'
readnames=readnames[:-1]
numread=len(readnames.split(';'))
return[chrom+'\t'+str(position)+'\t'+str(length)+'\t'+str(len(candi))+'\t'+str(numread)+'\t'+str(quality)+'\t'+readnames]
else:
return []
def counttimesort(a):
return [int(a.split('\t')[1]),int(a.split('\t')[2])]
def cluster(outpath,allsv,chrom,contiglength,mins,maxdepth,svtype,minmapq):
if allsv==[]:
return 0
t1=time.time()
# Large DEL
svtypeinfo={}
svtypeinfo['del']='Deletion';svtypeinfo['dup']='Duplication';svtypeinfo['inv']='Inversion'
svtypeinfo=svtypeinfo[svtype]
largesv=[c for c in allsv if int(c.split('\t')[2])>2000]
window=1600
largesv.sort(key=counttimesort)
largedel=[]
start=0
candi=[]
for event in largesv:
if int(event.split('\t')[1])<=start+window:
candi+=[event]
continue
if len(candi)>=mins:
largedel+=mergeinfo_insertion(candi,mins,svtypeinfo)
candi=[event]
start=int(event.split('\t')[1])
if len(candi)>=mins:
largedel+=mergeinfo_insertion(candi,mins,svtypeinfo)
candi=[]
#smaller DEL
allsv=[c for c in allsv if int(c.split('\t')[2])<=3000]
genomeposition=[0]*contiglength
for c in allsv:
start=int(c.split('\t')[1])
end=int(c.split('\t')[1])+int(c.split('\t')[2])
original=genomeposition[start-1:end-1]
new=[mm+1 for mm in original]
genomeposition[start-1:end-1]=new
svregion=[]
inblock=False
threshold=3
for i in range(len(genomeposition)):
if inblock:
if genomeposition[i]>=max(maxdep/10.0,threshold):
localdep+=[genomeposition[i]]
if genomeposition[i]>maxdep:
maxdep=genomeposition[i]
else:
inblock=False
end=i
if maxdep<=maxdepth:
peakpos=localdep.index(maxdep)
peakleftsize=0
for i in range(peakpos):
if localdep[peakpos-i-1]>=maxdep/10.0:
peakleftsize+=1
else:
break
svregion+=[(start+peakpos-peakleftsize,end,maxdep)]
start=0
end=0
maxdep=0
else:
if genomeposition[i] > threshold:
inblock=True
localdep=[genomeposition[i]]
start=i
maxdep=genomeposition[i]
svregion=[c for c in svregion if c[2] < maxdepth]
allsvinfo={}
for c in svregion:
allsvinfo[c]=[]
for c in allsv:
start=int(c.split('\t')[1])
end=start+int(c.split('\t')[2])
for d in svregion:
if min(end,d[1])-max(d[0],start)>0:
allsvinfo[d]+=[c]
sv=[]
for c in svregion:
svinfo=allsvinfo[c]
sv+=mergeinfo_insertion(svinfo,mins,svtypeinfo)
newsv=[]
for c in largedel:
testif=0
for d in sv:
if min(int(c.split('\t')[1])+int(c.split('\t')[2]), int(d.split('\t')[1])+int(d.split('\t')[2])) - max(int(c.split('\t')[1]),int(d.split('\t')[1]))>0 and 0.8*int(d.split('\t')[2])<=int(c.split('\t')[2])<=int(d.split('\t')[2])/0.8:
testif=1; break
if testif==0:
newsv+=[c]
newsv+=sv
newsv.sort(key=counttimesort)
t2=time.time()
print (chrom,'-',svtype,' finished, time cost: ',t2-t1)
if newsv!=[]:
f=open(outpath+svtype+'-merged-cluster-'+chrom,'w')
for c in newsv:
if minmapq==None:
if float(c.split('\t')[5])<1 or float(c.split('\t')[5])>=10:
f.write(c+'\n')
else:
if float(c.split('\t')[5])>=minmapq:
f.write(c+'\n')
f.close()
return 0
def cluster_ins(outpath,allsv,chrom,contiglength,mins,maxdepth,minmapq):
if allsv==[]:
return 0
t1=time.time()
svtypeinfo='Insertion'
# Large INS
largesv=[c for c in allsv if int(c.split('\t')[2])>2000]
window=1600
largesv.sort(key=counttimesort)
largedel=[]
start=0
candi=[]
for event in largesv:
if int(event.split('\t')[1])<=start+window:
candi+=[event]
continue
if len(candi)>=mins:
largedel+=mergeinfo_insertion(candi,mins,svtypeinfo)
candi=[event]
start=int(event.split('\t')[1])
if len(candi)>=mins:
largedel+=mergeinfo_insertion(candi,mins,svtypeinfo)
candi=[]
# Small INS
allsv=[c for c in allsv if int(c.split('\t')[2])<=3000]
genomeposition=[0]*contiglength
for c in allsv:
start=int(c.split('\t')[1])-100
end=int(c.split('\t')[1])+100
original=genomeposition[start-1:end-1]
new=[mm+1 for mm in original]
genomeposition[start-1:end-1]=new
svregion=[]
inblock=False
threshold=3
for i in range(len(genomeposition)):
if inblock:
if genomeposition[i]>=max(maxdep/10.0,threshold):
localdep+=[genomeposition[i]]
if genomeposition[i]>maxdep:
maxdep=genomeposition[i]
else:
inblock=False
end=i
if maxdep<=maxdepth:
peakpos=localdep.index(maxdep)
peakleftsize=0
for i in range(peakpos):
if localdep[peakpos-i-1]>=maxdep/10.0:
peakleftsize+=1
else:
break
svregion+=[(start+peakpos-peakleftsize,end,maxdep)]
start=0
end=0
maxdep=0
else:
if genomeposition[i] > threshold:
inblock=True
localdep=[genomeposition[i]]
start=i
maxdep=genomeposition[i]
svregion=[c for c in svregion if c[2] < maxdepth]
allsvinfo={}
for c in svregion:
allsvinfo[c]=[]
for c in allsv:
start=int(c.split('\t')[1])-50
end=start+100
for d in svregion:
if min(end,d[1])-max(d[0],start)>0:
allsvinfo[d]+=[c]
sv=[]
for c in svregion:
svinfo=allsvinfo[c]
mergedins=mergeinfo_insertion(svinfo,mins,svtypeinfo)
for m in mergedins:
sv+=[m+'\t'+chrom+'\t'+str(c[0])+'\t'+str(c[1])+'\t'+str(c[2])]
newsv=[]
for c in largedel:
testif=0
for d in sv:
if min(int(c.split('\t')[1])+int(c.split('\t')[2]), int(d.split('\t')[1])+int(d.split('\t')[2])) - max(int(c.split('\t')[1]),int(d.split('\t')[1]))>0 and 0.8*int(d.split('\t')[2])<=int(c.split('\t')[2])<=int(d.split('\t')[2])/0.8:
testif=1; break
if testif==0:
newsv+=[c]
newsv+=sv
newsv.sort(key=counttimesort)
t2=time.time()
print (chrom,'-ins finished, time cost: ',t2-t1)
if newsv!=[]:
f=open(outpath+'ins-merged-cluster-'+chrom,'a')
for c in newsv:
if minmapq==None:
if float(c.split('\t')[5])<1 or float(c.split('\t')[5])>=10:
f.write(c+'\n')
else:
if float(c.split('\t')[5])>=minmapq:
f.write(c+'\n')
f.close()
return 0