def read_next(inf,strata):
while True:
v = inf.readline()
if not v: return False
num = int(v.rstrip().split("\t")[3])
if num < strata: continue
arr = v.split("\t")
res = Bed(arr[0],int(arr[1]),int(arr[2]))
res.set_payload(int(num))
return res
def get_overlap(fileA,fileB,min_A,min_B):
infA = do_open(fileA)
infB = do_open(fileB)
bufA = read_next(infA,min_A)
bufB = read_next(infB,min_B)
tot = 0
sizeA = 0
sizeB = 0
if bufA:
sizeA = bufA.length()
if bufB:
sizeB = bufB.length()
zA = 1
zB = 1
while True:
#if (zA%10000 ==0 or zB%10000==0): sys.stderr.write(str(zA)+" "+str(zB)+" \r")
if not bufA or not bufB: break
c = bufA.cmp(bufB)
if c == 0:
tot += bufA.overlap_size(bufB)
saveA = bufA
nA = bufA.subtract(bufB)
if len(nA) > 0 and nA[-1].end == bufA.end:
num = bufA.get_payload()
bufA = Bed(nA[-1].chr,nA[-1].start-1,nA[-1].end)
bufA.set_payload(num)
else:
bufA = read_next(infA,min_A)
if bufA:
sizeA += bufA.length()
zA+=1
nB = bufB.subtract(saveA)
if len(nB) > 0 and nB[-1].end == bufB.end:
num = bufB.get_payload()
bufB = Bed(nB[-1].chr,nB[-1].start-1,nB[-1].end)
bufB.set_payload(num)
else:
bufB = read_next(infB,min_B)
if bufB:
sizeB += bufB.length()
zB+=1
elif c == -1:
bufA = read_next(infA,min_A)
if bufA:
sizeA += bufA.length()
zA += 1
else:
bufB = read_next(infB,min_B)
if bufB:
sizeB += bufB.length()
zB += 1
#sys.stderr.write("\n")
if bufA:
while True:
bufA = read_next(infA,min_A)
if bufA: sizeA += bufA.length()
else: break
if bufB:
while True:
bufB = read_next(infB,min_B)
if bufB: sizeB += bufB.length()
else: break
infA.close()
infB.close()
return [min_A,min_B,sizeA,sizeB,tot]