def addBackDeleted(recovSeq, f2,readSortedf2, noisyReads, parameterRobot):
newRecovSeq = np.zeros(len(recovSeq)*2, dtype= np.int64)
W = int(100*parameterRobot.L/2000)
counter = 0
for eachindex in range(len(recovSeq)-1):
KmerIndex = recovSeq[eachindex]
currentList =bridgeResolve.obtainReadDetail(KmerIndex, f2)
KmerIndex = recovSeq[eachindex+1 ]
nextList =bridgeResolve.obtainReadDetail(KmerIndex, f2)
countDiffMax,readListOfInterest = countDiff(currentList, nextList,W)
if countDiffMax >1 :
#print "countDiffMax", countDiffMax
for dummy in range(countDiffMax):
newKmerIndex = findIndex(readListOfInterest, f2,readSortedf2, dummy)
newRecovSeq[counter+ dummy] = newKmerIndex
counter = counter + countDiffMax
elif countDiffMax == 1 :
newRecovSeq[counter] = currentList[0][0]
counter = counter + 1
return newRecovSeq[0:counter]
def segmentedAdd(recovSeq, f2 ,readSortedf2, noisyReads, parameterRobot):
try :
recovSeqNew = np.zeros(2*len(recovSeq), dtype = np.int64)
thres = 2
W = int(100*parameterRobot.L/2000)
#print "W", W
counter = 0
runningSum = 0
while counter< len(recovSeq)-W:
KmerIndex = recovSeq[counter]
currentList =bridgeResolve.obtainReadDetail(KmerIndex, f2)
KmerIndex = recovSeq[counter+W ]
nextList =bridgeResolve.obtainReadDetail(KmerIndex, f2)
countDiffMax, readListOfInterest = countDiff(currentList, nextList, W, 5)
skip = checkSkip(currentList)
if (not skip and -thres <=countDiffMax - W <= thres) or countDiffMax ==0 or len(readListOfInterest) == 0:
recovSeqNew[runningSum] = recovSeq[counter]
counter += 1
runningSum += 1
else:
for dummy in range(countDiffMax):
newKmerIndex = findIndex(readListOfInterest, f2,readSortedf2, dummy)
recovSeqNew[runningSum+ dummy] = newKmerIndex
#print "counter, runningSum", counter ,runningSum
counter = counter + W
runningSum += countDiffMax
for counter in range(len(recovSeq)-W, len(recovSeq)):
recovSeqNew[runningSum] = recovSeq[counter]
runningSum += 1
except Exception:
print "recovSeqNew[runningSum+ dummy] = newKmerIndex ", len(recovSeqNew), runningSum, dummy, newKmerIndex
return recovSeqNew[0:runningSum]
def convertSeqtoBase(recovSeq, f2, noisyReads, parameterRobot):
correctedGen = np.zeros(len(recovSeq), dtype = np.int8)
for eachindex in range(len(recovSeq)):
KmerIndex = recovSeq[eachindex]
readsList =bridgeResolve.obtainReadDetail(KmerIndex, f2)
if len(readsList) == 0:
print len(readsList), eachindex
readNum, offset = readsList[0][1:3]
correctedGen[eachindex] = noisyReads[readNum][offset]
return correctedGen
def deleteExtra(recovSeq, f2, noisyReads, parameterRobot):
newRecovSeq = np.zeros(len(recovSeq), dtype = np.int64)
thresTrue = 3
counter = 0
for eachindex in range(len(recovSeq)):
KmerIndex = recovSeq[eachindex]
readsList =bridgeResolve.obtainReadDetail(KmerIndex, f2)
if len(readsList) >= thresTrue:
newRecovSeq[counter] = KmerIndex
counter = counter + 1
return newRecovSeq[0:counter]
def reportRecovSeqOriginal(recovSeq, f2, noisyReads, parameterRobot):
thresTrust = 50
G = parameterRobot.G
f2 = sorted(f2)
recoveredGenome = np.zeros(2*G,dtype = np.int8)
correctedGen = np.zeros(G, dtype = np.int8)
# -1 : fused, 0 : Snps
print "len(recovSeq)", len(recovSeq)
### MajorityVote
runningIndex = 0
for eachindex in range(len(recovSeq)):
KmerIndex = recovSeq[eachindex]
readsList =bridgeResolve.obtainReadDetail(KmerIndex, f2)
if eachindex % thresTrust == 0 :
readNum, offset = readsList[0][1:3]
recoveredGenome[runningIndex : runningIndex+ thresTrust] = noisyReads[readNum][offset: offset + thresTrust]
runningIndex += thresTrust
correctedGen= recoveredGenome[0:runningIndex]
print correctedGen[-10:-1], len(correctedGen)
countfused = 0
countsnps = 0
for eachitem in correctedGen:
if eachitem == -1 :
countfused = countfused +1
if eachitem == 0:
countsnps = countsnps +1
print "correctedGen[0:30]" ,correctedGen[0:30] , len(correctedGen)
print "Not corrected yet", countfused, countsnps
return correctedGen[0:int(G*1.1)]
