def performPhasing(folderName, mummerLink):
print "performPhasing"
'''
1. Interface from alignmentBridge.py :
shortToLongMap = formRelatedMap(f2, noisyReads, currentNode, indelRobot, toProcessList)
cleaner.cleaning([noisyReads,noisyReads] ,shortToLongMap, toProcessList,indelRobot, "init")
in1List, in2List, out1List, out2List, commonList, longReadToUse = cleaner.cleaning([noisyReads, noisyReads],shortToLongMap, toProcessList,indelRobot, "vote")
extendResult = extender.readExtender(in1List, in2List, out1List, out2List, commonList,indelRobot,longReadToUse, True)
2. Format of input data data :
bigDumpList.append([flankingList, repeatList, repeatPathway, flankingPathsList])
3. IO :
a) Input :
repeatSpecification.txt, phasingSeedName_Double.fasta, graph G
b) Output :
improved4.fasta
3. Algorithm:
a) reformatNoisyReads
b) reformatToProcessList
c) formShortToLongMapping
'''
json_data = open(folderName + 'repeatSpecification.txt', 'r')
loadData = json.load(json_data)
G = commonLib.seqGraph(0)
G.loadFromFile(folderName, "phaseStringGraph1")
lenDicRR = commonLib.obtainLength(folderName, "phasingSeedName_Double.fasta")
lenDicCC = commonLib.obtainLength(folderName, "improved3_Double.fasta")
N1 = len(lenDicCC)
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
for eachitem in loadData:
print eachitem
flankingList, repeatList, repeatPathway, flankingPathsList = eachitem[0], eachitem[1], eachitem[2], eachitem[3]
noisyReads, dicToOriginal, dicFromOriginal = reformatNoisyReads(folderName, flankingList, repeatList, N1)
toProcessList = reformatToProcessList(folderName , flankingList, repeatList, dicFromOriginal, N1)
shortToLongMap = formShortToLongMapping(folderName, G, toProcessList, dicFromOriginal,dicToOriginal, lenDicCR, N1 )
indelRobot = createIndelRobot(folderName)
cleaner.cleaning([noisyReads, noisyReads] , shortToLongMap, toProcessList, indelRobot, "init")
in1List, in2List, out1List, out2List, commonList, longReadToUse = cleaner.cleaning([noisyReads, noisyReads], shortToLongMap, toProcessList, indelRobot, "vote")
extendResult = extender.readExtender(in1List, in2List, out1List, out2List, commonList, indelRobot, longReadToUse, True)
if extendResult != -1:
print "extendResult: ", extendResult
assert(1==2)
def indelMSABridging(f2, currentNode,noisyReads,p, snpRate,flankinglen, parameterRobot):
# Need to loop over all the xnodes
canResolve, kmerPairsList = False, []
# Using contig Creator
indelRobot = common.parameterRobot()
indelRobot.defaultFolder = parameterRobot.defaultFolder
indelRobot.setReadStat( Nshort= parameterRobot.N, Nlong= parameterRobot.N, Lshort= parameterRobot.L, Llong= parameterRobot.L, p= parameterRobot.p , longOnly = True)
indelRobot.setGenomeStat(G = parameterRobot.G, lrep=500, lsnp=200, lint=50 )
indelRobot.setThresholdPara(liid = 30, thresForRandom= 0.5,thresForins =0.4, thresFordel=0.4, insMin=4, delMin=4,thresholdForSupport= 0.15, subthreshold= 9, editsub= -10, editins= -1, editdel= -1, editmatch = 1, lookRange =15)
#indelRobot.tunePara()
indelRobot.snprate = snpRate
# toProcessList : in1IndexList, in2IndexList, out1IndexList, out2IndexList, commonIndexList
# shortToLongMap : indexlong indexshort jstart jend istart iend
shortToLongMap,toProcessList = [], []
toProcessList = formToProcessList(f2, noisyReads, currentNode, indelRobot, flankinglen)
if len(toProcessList[4] ) == 0 :
return False, []
shortToLongMap = formRelatedMap(f2, noisyReads, currentNode, indelRobot, toProcessList)
cleaner.cleaning([noisyReads,noisyReads] ,shortToLongMap, toProcessList,indelRobot, "init")
in1List, in2List, out1List, out2List, commonList, longReadToUse = cleaner.cleaning([noisyReads, noisyReads],shortToLongMap, toProcessList,indelRobot, "vote")
extendResult = extender.readExtender(in1List, in2List, out1List, out2List, commonList,indelRobot,longReadToUse, True)
if extendResult == 0 :
canResolve = True
edgeWt = currentNode.listOfPrevNodes[0][1]
inKmerIndex = currentNode.listOfPrevNodes[0][0].nodeIndexList[-(edgeWt +1)]
edgeWt = currentNode.listOfNextNodes[0][1]
outKmerIndex = currentNode.listOfNextNodes[0][0].nodeIndexList[edgeWt ]
kmerPairsList.append([inKmerIndex,outKmerIndex ])
edgeWt = currentNode.listOfPrevNodes[1][1]
inKmerIndex = currentNode.listOfPrevNodes[1][0].nodeIndexList[-(edgeWt +1)]
edgeWt = currentNode.listOfNextNodes[1][1]
outKmerIndex = currentNode.listOfNextNodes[1][0].nodeIndexList[edgeWt ]
kmerPairsList.append([inKmerIndex,outKmerIndex ])
elif extendResult == 1 :
canResolve = True
edgeWt = currentNode.listOfPrevNodes[0][1]
inKmerIndex = currentNode.listOfPrevNodes[0][0].nodeIndexList[-(edgeWt +1)]
edgeWt = currentNode.listOfNextNodes[1][1]
outKmerIndex = currentNode.listOfNextNodes[1][0].nodeIndexList[edgeWt ]
kmerPairsList.append([inKmerIndex,outKmerIndex ])
edgeWt = currentNode.listOfPrevNodes[1][1]
inKmerIndex = currentNode.listOfPrevNodes[1][0].nodeIndexList[-(edgeWt +1)]
edgeWt = currentNode.listOfNextNodes[0][1]
outKmerIndex = currentNode.listOfNextNodes[0][0].nodeIndexList[edgeWt ]
kmerPairsList.append([inKmerIndex,outKmerIndex ])
elif extendResult == -1:
canResolve = False
kmerPairsList = []
print kmerPairsList
return canResolve, kmerPairsList
def indelMSABridging(f2, currentNode, noisyReads, p, snpRate, flankinglen,
parameterRobot):
# Need to loop over all the xnodes
canResolve, kmerPairsList = False, []
# Using contig Creator
indelRobot = common.parameterRobot()
indelRobot.defaultFolder = parameterRobot.defaultFolder
indelRobot.setReadStat(Nshort=parameterRobot.N,
Nlong=parameterRobot.N,
Lshort=parameterRobot.L,
Llong=parameterRobot.L,
p=parameterRobot.p,
longOnly=True)
indelRobot.setGenomeStat(G=parameterRobot.G, lrep=500, lsnp=200, lint=50)
indelRobot.setThresholdPara(liid=30,
thresForRandom=0.5,
thresForins=0.4,
thresFordel=0.4,
insMin=4,
delMin=4,
thresholdForSupport=0.15,
subthreshold=9,
editsub=-10,
editins=-1,
editdel=-1,
editmatch=1,
lookRange=15)
#indelRobot.tunePara()
indelRobot.snprate = snpRate
# toProcessList : in1IndexList, in2IndexList, out1IndexList, out2IndexList, commonIndexList
# shortToLongMap : indexlong indexshort jstart jend istart iend
shortToLongMap, toProcessList = [], []
toProcessList = formToProcessList(f2, noisyReads, currentNode, indelRobot,
flankinglen)
if len(toProcessList[4]) == 0:
return False, []
shortToLongMap = formRelatedMap(f2, noisyReads, currentNode, indelRobot,
toProcessList)
cleaner.cleaning([noisyReads, noisyReads], shortToLongMap, toProcessList,
indelRobot, "init")
in1List, in2List, out1List, out2List, commonList, longReadToUse = cleaner.cleaning(
[noisyReads, noisyReads], shortToLongMap, toProcessList, indelRobot,
"vote")
extendResult = extender.readExtender(in1List, in2List, out1List, out2List,
commonList, indelRobot, longReadToUse,
True)
if extendResult == 0:
canResolve = True
edgeWt = currentNode.listOfPrevNodes[0][1]
inKmerIndex = currentNode.listOfPrevNodes[0][0].nodeIndexList[-(
edgeWt + 1)]
edgeWt = currentNode.listOfNextNodes[0][1]
outKmerIndex = currentNode.listOfNextNodes[0][0].nodeIndexList[edgeWt]
kmerPairsList.append([inKmerIndex, outKmerIndex])
edgeWt = currentNode.listOfPrevNodes[1][1]
inKmerIndex = currentNode.listOfPrevNodes[1][0].nodeIndexList[-(
edgeWt + 1)]
edgeWt = currentNode.listOfNextNodes[1][1]
outKmerIndex = currentNode.listOfNextNodes[1][0].nodeIndexList[edgeWt]
kmerPairsList.append([inKmerIndex, outKmerIndex])
elif extendResult == 1:
canResolve = True
edgeWt = currentNode.listOfPrevNodes[0][1]
inKmerIndex = currentNode.listOfPrevNodes[0][0].nodeIndexList[-(
edgeWt + 1)]
edgeWt = currentNode.listOfNextNodes[1][1]
outKmerIndex = currentNode.listOfNextNodes[1][0].nodeIndexList[edgeWt]
kmerPairsList.append([inKmerIndex, outKmerIndex])
edgeWt = currentNode.listOfPrevNodes[1][1]
inKmerIndex = currentNode.listOfPrevNodes[1][0].nodeIndexList[-(
edgeWt + 1)]
edgeWt = currentNode.listOfNextNodes[0][1]
outKmerIndex = currentNode.listOfNextNodes[0][0].nodeIndexList[edgeWt]
kmerPairsList.append([inKmerIndex, outKmerIndex])
elif extendResult == -1:
canResolve = False
kmerPairsList = []
print kmerPairsList
return canResolve, kmerPairsList