def xResolve(self, xResolvedList):
self.mapDummyToRealDic = {}
self.xResolvedSimplifiedList = []
for i in range(self.N1):
for y in xResolvedList[i]:
inNode = y[0]
outNode = y[-1]
for eachprev in self.graphNodesList[i].listOfPrevNodes:
key = eachprev[0]
if key >= self.N1 and self.mapDummyToRealDic[key-self.N1][0] == y[0]:
inNode = key
for eachnext in self.graphNodesList[i].listOfNextNodes:
key = eachnext[0]
if key >= self.N1 and self.mapDummyToRealDic[key-self.N1][0] == y[-1]:
outNode = key
if len(self.graphNodesList[i].listOfPrevNodes) == 1 and len(self.graphNodesList[i].listOfNextNodes) ==1:
self.xResolvedSimplifiedList.append([inNode, i])
self.xResolvedSimplifiedList.append([i, outNode])
else:
self.graphNodesList.append(graphLib.seqGraphNode(self.N1+self.runningCtr))
if False:
toRemoveList = []
for outgo in self.graphNodesList[inNode].listOfNextNodes:
toRemoveList.append([inNode, outgo[0]])
for income in self.graphNodesList[outNode].listOfPrevNodes:
toRemoveList.append([income[0], outNode])
for eachpair in toRemoveList:
self.removeEdge(eachpair[0], eachpair[1])
else:
self.removeEdge(inNode,i )
self.removeEdge(i, outNode)
self.insertEdge(inNode, self.N1 + self.runningCtr, 1997)
self.insertEdge(self.N1 + self.runningCtr, outNode, 1997)
self.mapDummyToRealDic[self.runningCtr] = [ [i] , self.graphNodesList[i].nodeIndexList ]
self.xResolvedSimplifiedList.append([inNode, self.N1 + self.runningCtr])
self.xResolvedSimplifiedList.append([self.N1 + self.runningCtr, outNode])
self.runningCtr = self.runningCtr + 1
def xResolve(self, xResolvedList):
self.mapDummyToRealDic = {}
self.xResolvedSimplifiedList = []
for i in range(self.N1):
for y in xResolvedList[i]:
inNode = y[0]
outNode = y[-1]
for eachprev in self.graphNodesList[i].listOfPrevNodes:
key = eachprev[0]
if key >= self.N1 and self.mapDummyToRealDic[key-self.N1][0] == y[0]:
inNode = key
for eachnext in self.graphNodesList[i].listOfNextNodes:
key = eachnext[0]
if key >= self.N1 and self.mapDummyToRealDic[key-self.N1][0] == y[-1]:
outNode = key
if len(self.graphNodesList[i].listOfPrevNodes) == 1 and len(self.graphNodesList[i].listOfNextNodes) ==1:
self.xResolvedSimplifiedList.append([inNode, i])
self.xResolvedSimplifiedList.append([i, outNode])
else:
self.graphNodesList.append(graphLib.seqGraphNode(self.N1+self.runningCtr))
if False:
toRemoveList = []
for outgo in self.graphNodesList[inNode].listOfNextNodes:
toRemoveList.append([inNode, outgo[0]])
for income in self.graphNodesList[outNode].listOfPrevNodes:
toRemoveList.append([income[0], outNode])
for eachpair in toRemoveList:
self.removeEdge(eachpair[0], eachpair[1])
else:
self.removeEdge(inNode,i )
self.removeEdge(i, outNode)
self.insertEdge(inNode, self.N1 + self.runningCtr, 1997)
self.insertEdge(self.N1 + self.runningCtr, outNode, 1997)
self.mapDummyToRealDic[self.runningCtr] = [ [i] , self.graphNodesList[i].nodeIndexList ]
self.xResolvedSimplifiedList.append([inNode, self.N1 + self.runningCtr])
self.xResolvedSimplifiedList.append([self.N1 + self.runningCtr, outNode])
self.runningCtr = self.runningCtr + 1
def outputResults(folderName, mummerLink, toPhaseList, N1, G):
'''
Algorithm :
a) Write as contigs
b) Add back reverse complement
c) Create G2 as the readOut part
d) Output the contigs by a function call
'''
# a)
combinedName = "contigAndRead_Double.fasta"
os.system("cp " + folderName + "improved3_Double.fasta " + folderName + combinedName)
fout = open(folderName + combinedName, 'a')
fin = open(folderName + "phasingSeedName_Double.fasta", 'r')
tmp = fin.readline().rstrip()
while len(tmp) > 0:
if tmp[0] != ">":
fout.write(tmp + "\n")
else:
infoArr = tmp[5:].split("_")
fout.write(">Contig" + str(int(infoArr[0]) + N1 / 2))
fout.write("_" + infoArr[1] + "\n")
tmp = fin.readline().rstrip()
fin.close()
fout.close()
# b)
'''
[28], [[2, 690, 28], [6, 126, 28], [28, 212, 0], [28, 216, 4]], 1
[2 , 690, 28, 212, 0]
'''
completePhaseList = []
for eachitem in toPhaseList:
repeat = eachitem[-3]
flanking = eachitem[-2]
result = eachitem[-1]
revrepeat = []
for eachsub in eachitem[-3][-1::-1]:
revrepeat.append(eachsub + pow(-1, eachsub))
revflanking = [[] for i in range(4)]
for j in range(2):
for eachsub in eachitem[-2][j + 2][-1::-1]:
revflanking[j].append(eachsub + pow(-1, eachsub))
for eachsub in eachitem[-2][j][-1::-1]:
revflanking[j + 2].append(eachsub + pow(-1, eachsub))
revresult = eachitem[-1]
completePhaseList.append([repeat, flanking, result])
completePhaseList.append([revrepeat, revflanking, revresult])
print "completePhaseList", completePhaseList
# c)
G2 = graphLib.seqGraph(N1)
nameDic = {}
for i in range(N1):
nameDic[i] = i
for eachitem in completePhaseList:
repeat, flanking, result = eachitem[0] , eachitem[1] , eachitem[2]
path = [[], []]
if result == 0:
path[0] = flanking[0][0:-1] + repeat + flanking[2][1:]
path[1] = flanking[1][0:-1] + repeat + flanking[3][1:]
else:
path[0] = flanking[0][0:-1] + repeat + flanking[3][1:]
path[1] = flanking[1][0:-1] + repeat + flanking[2][1:]
print path[0] , path[1]
for i in range(2):
eachpath = path[i]
currentNode = G2.graphNodesList[eachpath[0]]
for nextNodeIndex, ctr in zip(eachpath[1:], range(len(eachpath[1:]))):
if ctr != len(eachpath[1:]) - 1:
myindex = len(G2.graphNodesList)
nameDic[myindex] = nextNodeIndex
newNode = graphLib.seqGraphNode(myindex)
G2.graphNodesList.append(newNode)
else:
newNode = G2.graphNodesList[nextNodeIndex]
wt = 0
for eachck in G.graphNodesList[nameDic[currentNode.nodeIndex]].listOfNextNodes:
if eachck[0] == nextNodeIndex:
wt = eachck[1]
break
newNode.listOfPrevNodes.append([currentNode.nodeIndex, wt])
currentNode.listOfNextNodes.append([newNode.nodeIndex, wt])
currentNode = newNode
graphFileName = "phaseGraphFinal"
G2.condense()
G2.saveToFile(folderName, graphFileName)
IORobot.readContigOut(folderName, mummerLink, graphFileName, combinedName, "improved4.fasta", "outOpenListphaing", nameDic)
