def testBandedClustering():
dummyParameters = logging.parameterObj()
#dummyParameters.defaultFolder = ""
dummyParameters.liid = 40
dummyParameters.K = 40
dummyParameters.threshold = 6
dummyParameters.p = 0.015
dummyParameters.indel = True
dummyParameters.N, dummyParameters.G, dummyParameters.L, dummyParameters.p, typeOfGen, detail = 600, 10000,200, 0.015, 'm', "500-200-50"
startFingerPrint, endFingerPrint, read1, read2 = [] , [] , [] , []
read1= np.zeros(200, dtype= np.int64)
read2 = np.zeros(200, dtype= np.int64)
for i in range(200):
read1[i] = random.randint(1,4)
read2[i] = random.randint(1,4)
for i in range(50):
read2[i] = 4
read1[150+i] = 4
print read1, read2
startFingerPrint, endFingerPrint = [160,8] ,[ 190,40]
score , returnalignedSeq1, returnalignedSeq2 , starti, startj , endi, endj =cluster.SWAlignmentBanded(startFingerPrint, endFingerPrint,read1 ,read2 , dummyParameters)
print "score", score
cluster.printSeq(returnalignedSeq1)
cluster.printSeq(returnalignedSeq2)
print "starti, startj, endi , endj : ", starti, startj, endi , endj
score , returnalignedSeq1, returnalignedSeq2 , starti, startj , endi, endj =cluster.SWAlignment(read1, read2 , dummyParameters)
print "score", score
cluster.printSeq(returnalignedSeq1)
cluster.printSeq(returnalignedSeq2)
print "starti, startj, endi , endj : ", starti, startj, endi , endj
def testBandedClustering():
dummyParameters = logging.parameterObj()
#dummyParameters.defaultFolder = ""
dummyParameters.liid = 40
dummyParameters.K = 40
dummyParameters.threshold = 6
dummyParameters.p = 0.015
dummyParameters.indel = True
dummyParameters.N, dummyParameters.G, dummyParameters.L, dummyParameters.p, typeOfGen, detail = 600, 10000, 200, 0.015, 'm', "500-200-50"
startFingerPrint, endFingerPrint, read1, read2 = [], [], [], []
read1 = np.zeros(200, dtype=np.int64)
read2 = np.zeros(200, dtype=np.int64)
for i in range(200):
read1[i] = random.randint(1, 4)
read2[i] = random.randint(1, 4)
for i in range(50):
read2[i] = 4
read1[150 + i] = 4
print read1, read2
startFingerPrint, endFingerPrint = [160, 8], [190, 40]
score, returnalignedSeq1, returnalignedSeq2, starti, startj, endi, endj = cluster.SWAlignmentBanded(
startFingerPrint, endFingerPrint, read1, read2, dummyParameters)
print "score", score
cluster.printSeq(returnalignedSeq1)
cluster.printSeq(returnalignedSeq2)
print "starti, startj, endi , endj : ", starti, startj, endi, endj
score, returnalignedSeq1, returnalignedSeq2, starti, startj, endi, endj = cluster.SWAlignment(
read1, read2, dummyParameters)
print "score", score
cluster.printSeq(returnalignedSeq1)
cluster.printSeq(returnalignedSeq2)
print "starti, startj, endi , endj : ", starti, startj, endi, endj
def checkBridgingFromReads(f2, xNode,frankingdepth, noisyReads, parameterRobot):
isBridged, matchingList = False, []
### Find bridging reads
bridgingReads = []
K = 150
searchdepth = 5
outList = findRangeList(xNode.nodeIndexList[K: K+searchdepth], f2 )
inList = findRangeList(xNode.nodeIndexList[frankingdepth:searchdepth + frankingdepth], f2 )
print "my name is Bond", outList
print inList
bridgingReads = isIntersectIndel(inList, outList, K - frankingdepth)
### Determine Extension List and isBridged or not
inputReads = [8 for i in range(len(xNode.listOfPrevNodes))]
outputReads = [8 for i in range(len(xNode.listOfNextNodes))]
inMap = []
outMap = []
threshold, liid,overhang= parameterRobot.threshold ,parameterRobot.liid ,5
speciallen = 40
for i in range(len(inputReads)):
tempList = obtainReadNum(xNode.listOfPrevNodes[i][0].nodeIndexList[-speciallen], f2)
tempList = sorted(tempList, key = itemgetter(1))
inputReads[i] = tempList[0][0]
print "In ",i , xNode.listOfPrevNodes[i][0].nodeIndexList[-1],inputReads[i], len(xNode.listOfPrevNodes[i][0].nodeIndexList)
for i in range(len(outputReads)):
tempList = obtainReadNum(xNode.listOfNextNodes[i][0].nodeIndexList[speciallen], f2)
tempList = sorted(tempList,key = itemgetter(1))
outputReads[i] = tempList[-1][0]
print "Out ",i , xNode.listOfNextNodes[i][0].nodeIndexList[0], outputReads[i], len(xNode.listOfNextNodes[i][0].nodeIndexList)
print "hi there", len(inputReads), len(outputReads), len(bridgingReads)
for prevIndex, dummyindex in zip(inputReads, range(len(inputReads))):
endNoisy1= 0
# print noisyReads[0][0]
# print prevIndex
# print endNoisy1
while (noisyReads[prevIndex][endNoisy1] != 0):
endNoisy1 += 1
for bridgeIndex in bridgingReads:
endNoisy2 =0
while (noisyReads[bridgeIndex][endNoisy2] != 0):
endNoisy2 += 1
score, returnalignedSeq1, returnalignedSeq2 , starti, startj , endi, endj = cluster.SWAlignment(noisyReads[prevIndex][0:endNoisy1], noisyReads[bridgeIndex][0:endNoisy2], parameterRobot)
check = cluster.meetRequirement(score, returnalignedSeq1, returnalignedSeq2 ,starti, startj, endi, endj, threshold, liid,overhang, endNoisy1, endNoisy2 )
if [prevIndex, bridgeIndex] == [1318, 235]:
print "strange"
print " starti, startj , endi, endj", starti, startj , endi, endj
cluster.printSeq(returnalignedSeq1)
cluster.printSeq(returnalignedSeq2)
if check :
inMap.append([prevIndex, bridgeIndex, 0, dummyindex])
print "inMap", inMap
for nextIndex,dummyindex in zip(outputReads,range(len(outputReads))):
endNoisy1= 0
while (noisyReads[nextIndex][endNoisy1] != 0):
endNoisy1 += 1
for bridgeIndex in bridgingReads:
endNoisy2 =0
while (noisyReads[bridgeIndex][endNoisy2] != 0):
endNoisy2 += 1
score, returnalignedSeq1, returnalignedSeq2 , starti, startj , endi, endj = cluster.SWAlignment(noisyReads[nextIndex][0:endNoisy1], noisyReads[bridgeIndex][0:endNoisy2], parameterRobot)
check = cluster.meetRequirement(score, returnalignedSeq1, returnalignedSeq2 ,starti, startj, endi, endj, threshold, liid,overhang, endNoisy1, endNoisy2)
if [nextIndex, bridgeIndex] == [235, 235]:
print "strange 2 "
print " starti, startj , endi, endj", starti, startj , endi, endj
cluster.printSeq(returnalignedSeq1)
cluster.printSeq(returnalignedSeq2)
if check :
outMap.append([nextIndex, bridgeIndex, 1, dummyindex])
print "outMap,", outMap
print "matchingList", matchingList
for eachinmap in inMap:
for eachoutmap in outMap:
if eachinmap[1] == eachoutmap[1] :
dummyIn = eachinmap[3]
dummyOut = eachoutmap[3]
print "dummyIn, dummyOut", dummyIn, dummyOut
#print "eachinmap", eachinmap
#print "eachoutmap",eachoutmap
edgeWt = xNode.listOfPrevNodes[dummyIn][1]
inKmerIndex = xNode.listOfPrevNodes[dummyIn][0].nodeIndexList[-(edgeWt+1 )]
edgeWt = xNode.listOfNextNodes[dummyOut][1]
outKmerIndex = xNode.listOfNextNodes[dummyOut][0].nodeIndexList[edgeWt]
matchingList.append([inKmerIndex,outKmerIndex ])
### Check isBridged
if len(matchingList) > 0 :
matchingList = distinct(matchingList)
reverseList = []
for eachitem in matchingList:
reverseList.append([eachitem[1], eachitem[0]])
if len(distinct(matchingList, "zero")) == len(inputReads) and len(distinct(reverseList, "zero")) == len(outputReads):
isBridged = True
else:
isBridged = False
#matchingList = [[28346, 32138], [28346, 4913], [30233, 32138]]
return isBridged, matchingList
