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benchmark_lib.py
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benchmark_lib.py
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import pysam
import sys
def calcOverlap(B1,E1,B2,E2):
if B1<=E2 and B1>=B2:
Overlap=min(E2-B1,E1-B1)
elif E1>=B2 and E1<=E2:
Overlap=E1-B2
elif B2>=B1 and B2<=E1:#1 covers 2
Overlap=E2-B2
else:
Overlap=-1
return Overlap
def inclusion(In1,In2):#return 0: not overlapped, 1: overlapped, 2: In1 include In2, 3: In2 inlcude In1, 4: identical
if In1==In2:
return 4
elif In1[0]>=In2[0] and In1[1]<=In2[1]:
return 3
elif In1[0]<=In2[0] and In1[1]>=In2[1]:
return 2
elif In1[0]>=In2[0] and In1[0]<=In2[1] or In1[1]>=In2[0] and In1[1]<=In2[1]:
return 1
return 0
class interval:
def __init__(self, chrom, start, end, type):
self.chrom = chrom
self.start = start
self.end = end
self.type = type
def __str__(self):
return "%s:%s-%s,%s,%s"%(self.chrom,self.start,self.end,self.end-self.start,self.type)
def get_chrom(self):
return self.chrom
def get_start(self):
return self.start
def get_end(self):
return self.end
def get_type(self):
return self.type
def get_length(self):
return self.end - self.start + 1
def is_overlap_pure(self, other, percent=0):
if self.start > other.get_end() or self.end < other.get_start():
return False
if self.start >= other.get_start():
if self.end <= other.get_end():
overlap = self.get_length()
else:
overlap = other.get_end() - self.start + 1
if float(overlap) / float(self.get_length()) >= percent and float(overlap) / float(other.get_length()) >= percent:
return True
else:
return False
if self.start < other.get_start():
if other.get_end() <= self.end:
overlap = other.get_length()
else:
overlap = self.end - other.get_start() + 1
if float(overlap) / float(self.get_length()) >= percent and float(overlap) / float(other.get_length()) >= percent:
return True
else:
return False
def is_overlap(self, other):
if self.chrom != other.get_chrom() or self.type != other.get_type():
return False
elif self.start > other.get_end() or self.end < other.get_start():
return False
else:
return True
def is_overlap_by_percent(self, other, percent):
if self.chrom != other.get_chrom() or self.type != other.get_type():
return False
if self.start > other.get_end() or self.end < other.get_start():
return False
if self.start >= other.get_start():
if self.end <= other.get_end():
overlap = self.get_length()
else:
overlap = other.get_end() - self.start + 1
if float(overlap) / float(self.get_length()) >= percent and float(overlap) / float(other.get_length()) >= percent:
return True
else:
return False
if self.start < other.get_start():
if other.get_end() <= self.end:
overlap = other.get_length()
else:
overlap = self.end - other.get_start() + 1
if float(overlap) / float(self.get_length()) >= percent and float(overlap) / float(other.get_length()) >= percent:
return True
else:
return False
def is_overlap_by_percent_or_near(self, other, percent, near):#for insertion, if break point is near within near considered overlapped
if self.chrom != other.get_chrom() or self.type != other.get_type():
return False
if self.type=="INS":
spoint=int((self.start+self.end)/2)
opoint=int((other.start+other.end)/2)
if abs(spoint-opoint)<=near:
return True
if self.start > other.get_end() or self.end < other.get_start():
return False
if self.start >= other.get_start():
if self.end <= other.get_end():
overlap = self.get_length()
else:
overlap = other.get_end() - self.start + 1
if float(overlap) / float(self.get_length()) >= percent and float(overlap) / float(other.get_length()) >= percent:
return True
else:
return False
if self.start < other.get_start():
if other.get_end() <= self.end:
overlap = other.get_length()
else:
overlap = self.end - other.get_start() + 1
if float(overlap) / float(self.get_length()) >= percent and float(overlap) / float(other.get_length()) >= percent:
return True
else:
return False
def is_included_by(self,other):
if self.start>=other.get_start() and self.end<=other.get_end():
return True
return False
def parse_cnvnator(input_file, min_length=0, max_length=sys.maxsize):
records = []
f = open(input_file, 'r')
for line in f:
record = line.split()
type = record[0]
chrom = record[1].split(':')[0]
region = record[1].split(':')[1].split('-')
start = int(region[0])
end = int(region[1])
if type == 'deletion':
tmp = interval(chrom, start, end, 'DEL')
if tmp.get_length() >= min_length and tmp.get_length() < max_length:
records.append(tmp)
if type == 'duplication':
tmp = interval(chrom, start, end, 'DUP')
if tmp.get_length() >= min_length and tmp.get_length() < max_length:
records.append(tmp)
f.close()
return records
class Match:
def __init__(self,Type=0,gs=None,Target=None):#Type:0:percent or near; 1:inclusion
self.Type=Type
self.gs=gs
self.Target=Target
self.gsp=0
self.tgp=0
self.analyze()
def addGS(self,gs):
self.gs=gs
self.analyze()
def addTarget(self,Target):
self.Target=Target
self.analyze()
def analyze(self):
if self.gs==None or self.Target==None:
return
Over=calcOverlap(self.gs.start,self.gs.end,self.Target.start,self.Target.end)
self.gsp=Over/(self.gs.end-self.gs.start)
self.tgp=Over/(self.Target.end-self.Target.start)
def __str__(self):
return "gs:%s,tg:%s,gsp:%d%%,tgp:%d%%"%(self.gs,self.Target,self.gsp*100,self.tgp*100)+(", gs included by tg"if self.gsp>=1 else "")+(", tg included by gs"if self.tgp>=1 else"")
def calculate_sensitivity_by_percent(goldstandard, callset, percent,near=-1,printmatch=False):
count = 0
gaincount=0
losscount=0
inscount=0
gaintotal=0
losstotal=0
instotal=0
results=[]
for interval1 in goldstandard:
if interval1.type=="DUP":
gaintotal+=1
elif interval1.type=="DEL":
losstotal+=1
elif interval1.type=="INS":
instotal+=1
tag = False
for interval2 in callset:
if interval1.type!=interval2.type:
continue
if interval1.is_overlap_by_percent_or_near(interval2, percent,near):
tag = True
results.append(Match(0,interval1,interval2))
if tag == True:
if printmatch:
print(interval1)
count = count + 1
if interval1.type=="DUP":
gaincount+=1
elif interval1.type=="DEL":
losscount+=1
elif interval1.type=="INS":
inscount+=1
print('All=%s, Found=%s, Recalled=%s(percentage=%s)' % (len(goldstandard),str(len(callset)),count,percent))
print('Sensitivity: All:%s, Dup:%s(%s/%s), Del:%s(%s/%s), Ins:%s(%s/%s)' %(str(float(count) / float(len(goldstandard))) if len(goldstandard)!=0 else "N/A",\
gaincount/gaintotal if gaintotal !=0 else "N/A",gaincount,gaintotal,\
losscount/losstotal if losstotal!=0 else "N/A",losscount,losstotal,\
inscount/instotal if instotal!=0 else "N/A",inscount,instotal))
return results
def calculate_fdr_by_percent(goldstandard, callset, percent, near=-1, printmatch=False):
count = 0
gaincount=0
losscount=0
inscount=0
gaintotal=0
losstotal=0
instotal=0
results=[]
for interval1 in callset:
if interval1.type=="DUP":
gaintotal+=1
elif interval1.type=="DEL":
losstotal+=1
elif interval1.type=="INS":
instotal+=1
tag = False
for interval2 in goldstandard:
if interval1.type!=interval2.type:
continue
if interval1.is_overlap_by_percent_or_near(interval2, percent,near):
tag = True
results.append(Match(0,interval2,interval1))
if tag == True:
if printmatch:
print(interval1)
count = count + 1
if interval1.type=="DUP":
gaincount+=1
elif interval1.type=="DEL":
losscount+=1
elif interval1.type=="INS":
inscount+=1
print('All=%s, Found=%s, Correct=%s(percentage=%s)' % (len(goldstandard),str(len(callset)),count,percent))
print('FDR(Right/All): All:%s, Dup:%s(%s/%s), Del:%s(%s/%s), Ins:%s(%s/%s)' \
%(str(1-float(count) / float(len(callset))) if len(callset)!=0 else "N/A",1-gaincount/gaintotal if gaintotal !=0 else "N/A",gaincount,gaintotal,\
1-losscount/losstotal if losstotal!=0 else "N/A",losscount,losstotal,\
1-inscount/instotal if instotal!=0 else "N/A",inscount,instotal))
return results
##consider caught if callset fully include goldstandard
def calculate_sensitivity_by_inclusion(goldstandard, callset, printmatch=False):
count = 0
gaincount=0
losscount=0
inscount=0
gaintotal=0
losstotal=0
instotal=0
results=[]
for interval1 in goldstandard:
if interval1.type=="DUP":
gaintotal+=1
elif interval1.type=="DEL":
losstotal+=1
elif interval1.type=="INS":
instotal+=1
tag = False
for interval2 in callset:
if interval1.type!=interval2.type:
continue
if interval1.is_included_by(interval2) or interval2.is_included_by(interval1):
results.append(Match(1,interval1,interval2))
tag = True
if tag == True:
if printmatch:
print(interval1)
count = count + 1
if interval1.type=="DUP":
gaincount+=1
elif interval1.type=="DEL":
losscount+=1
elif interval1.type=="INS":
inscount+=1
print('All=%s, Found=%s, Recalled=%s(by inclusion)' % (len(goldstandard),str(len(callset)),count))
print('Sensitivity: All:%s, Dup:%s(%s/%s), Del:%s(%s/%s), Ins:%s(%s/%s)' %(str(float(count) / float(len(goldstandard)))if len(goldstandard)!=0 else "N/A",\
gaincount/gaintotal if gaintotal !=0 else "N/A",gaincount,gaintotal,\
losscount/losstotal if losstotal!=0 else "N/A",losscount,losstotal,\
inscount/instotal if instotal!=0 else "N/A",inscount,instotal))
return results
def calculate_fdr_by_inclusion(goldstandard, callset, printmatch=False):
count = 0
gaincount=0
losscount=0
inscount=0
gaintotal=0
losstotal=0
instotal=0
results=[]
for interval1 in callset:
if interval1.type=="DUP":
gaintotal+=1
elif interval1.type=="DEL":
losstotal+=1
elif interval1.type=="INS":
instotal+=1
tag = False
for interval2 in goldstandard:
if interval1.type!=interval2.type:
continue
if interval2.is_included_by(interval1) or interval1.is_included_by(interval2):
tag = True
results.append(Match(1,interval2,interval1))
if tag == True:
if printmatch:
print(interval1)
count = count + 1
if interval1.type=="DUP":
gaincount+=1
elif interval1.type=="DEL":
losscount+=1
elif interval1.type=="INS":
inscount+=1
print('All=%s, Found=%s, Correct=%s(by inclusion)' % (len(goldstandard),str(len(callset)),count))
print('FDR(Right/All): All:%s, Dup:%s(%s/%s), Del:%s(%s/%s), Ins:%s(%s/%s)' \
%(str(1-float(count) / float(len(callset))) if len(callset)!=0 else "N/A",1-gaincount/gaintotal if gaintotal !=0 else "N/A",gaincount,gaintotal,\
1-losscount/losstotal if losstotal!=0 else "N/A",losscount,losstotal,\
1-inscount/instotal if instotal!=0 else "N/A",inscount,instotal))
return results
def parse_vcf(filename,contigs=None,samples=None):
vcf=pysam.VariantFile(filename,"r")
result=[]
included={}
includedSamples={}
if contigs!=None:
for c in contigs:
included[c]=True
if samples!=None:
for s in samples:
includedSamples[s.upper()]=True
for record in vcf.fetch():
End=record.pos
try:
End=record.pos+abs(record.info["SVLEN"])
except:
try:
End=record.pos+abs(record.info["SVLEN"][0])
except:
try:
End=record.info["END"]
except:
try:
End=record.stop
except:
pass
try:
chrom=record.chrom
if samples!=None and len(samples)==1:
sa=None
#if len(record.chrom)<3 and (int(record.chrom[:2])<23 or record.chrom.upper()=="X" or record.chrom.upper()=="Y"):
# chrom="chr"+record.chrom
if contigs!=None:
if not chrom in included.keys():
continue
if samples!=None:
try:
skip=True
if len(record.samples)!=0:
for s in record.samples:
if record.samples[s].name in includedSamples.keys() or (len(samples)==1 and samples[0] in record.samples[s].name):
if record.samples[s].allele_indices!=(0,0):
sa=record.samples[s].allele_indices
skip=False
if skip:
continue
else:
if not (record.info["SAMPLE"].upper() in includedSamples.keys() or (len(samples)==1 and samples[0] in record.info["SAMPLE"])):
continue
except Exception as e:
continue
temp=None
if abs(record.pos-24326713)<2:
a=1
if record.info["SVTYPE"]=="INS":
temp=interval(chrom,record.pos,record.stop+1,"INS")
elif record.info["SVTYPE"]=="DEL":
temp=interval(chrom,record.pos,End,"DEL")
elif record.info["SVTYPE"]=="DUP":
temp=interval(chrom,record.pos,End,"DUP")
elif record.info["SVTYPE"]=="CNV":
CNs=[]
for a in record.alts:
if "<CN" in a:
CNs.append(int(a[a.find("<CN")+3:-1]))
else:
CNs.append(1)
if len(CNs)==0:
continue
if len(CNs)>1:
Type="CNV"
if samples!=None and len(samples)==1:
Al=1
if sa[0]==0:
Al=CNs[sa[1]-1]
if sa[1]==0:
Al=CNs[sa[0]-1]
if sa[0]==sa[1]:
Al=CNs[sa[0]-1]
if Al==0:
Type="DEL"
elif Al>1:
Type="DUP"
elif CNs[0]==0:
Type="DEL"
else:
Type="DUP"
temp=interval(chrom,record.pos,End,Type)
else:
continue
result.append(temp)
except:
pass
vcf.close()
return result
def parse_my(filename,contigs=None, samples=None, format=None):
if format.upper()=="VCF" or filename[-4:]==".vcf" or filename[-4:]==".bcf":
return parse_vcf(filename,contigs,samples)
myout=open(filename,"r")
records=[]
for line in myout:
try:
line=line.replace(" ","")
sl=line.split(",")
blockstart=int(sl[0].split("-")[0].split(":")[1])
blockend=int(sl[0].split("-")[1].split(":")[1])
breakstart=int(sl[2].split(":")[-1])
breakend=int(sl[3].split(":")[1].split("]")[0])
temp=interval(sl[0].split(":")[0],breakstart,breakend,"DEL" if sl[1]=="DEL" else ("INS" if sl[1]=="INS" else "DUP"))
vsamples=sl[-2].split()
skip=True
for s in samples:
for v in vsamples:
if s in v:
skip=False
if skip:
continue
records.append(temp)
except:
continue
myout.close()
return records