def formReverseGraph(G):
nNode = len(G.graphNodesList)
Grev = commonLib.seqGraph(nNode)
for i in range(nNode):
for j in range(nNode):
haveInserted = commonLib.nameInEdgeList(j, G.graphNodesList[i].listOfNextNodes)
if haveInserted:
Grev.insertEdge(j, i, 100)
return Grev
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 connectContigs(toPhase, toRemove, toBR, folderName, mummerLink):
print "\nConnect Contigs"
tmpList = []
delThres =20000
lenDic = commonLib.obtainLength(folderName, "improved3_Double.fasta")
for eachitem in toRemove:
tmpList.append(eachitem/2)
tmpList.sort()
removeContigIndexList = []
for key, items in groupby(tmpList):
name = "Contig"+ str(key)+"_p"
if lenDic[name] < delThres:
removeContigIndexList.append(2*key)
removeContigIndexList.append(2*key+1)
print "removeContigIndexList", removeContigIndexList
### toRemove ===> remove both strand when detected
G = commonLib.seqGraph(len(lenDic))
### hack ! make the nodeIndexList to be empty for empty nodes
for eachnode in G.graphNodesList:
if eachnode.nodeIndex in removeContigIndexList:
eachnode.nodeIndexList = []
# form a graph, .condense, then use readContigOut
### add edge
for eachedge in toBR:
i = eachedge[0]/2
j = eachedge[1]/2
wt = eachedge[3]+1
print "i, j, wt", i, j, wt
G.insertEdge(i, j, wt)
tmpFileName = "xphasebonus"
G.condense()
G.saveToFile(folderName,tmpFileName )
commonLib.readContigOut(folderName, mummerLink, tmpFileName, "improved3_Double.fasta", "improved4.fasta", tmpFileName+"Open")
def defineRepeatAndFlanking(folderName, mummerLink,contigFilename,contigReadGraph,repeatFilename,repeatSpec ):
'''
Input :
V a) String graph : G
V b) Repeat Pairing : repeatList
Output :
V a) chain of repeat indices (e.g. [S= R1, R33, R45, R24= E])
V b) chain of flanking region indices for in1/2 out1/2 middle (e.g. [C1, R2, R4] )
V c) in1/2 out1/2 and middle reads per repeat (e.g. [R1, R33, R45, R24])
Algorithm :
V 1. Find repeat by graph operations
V 2. Find flanking region by graph operations
V 3. Find associated reads by graph operations
'''
print "defineRepeatAndFlanking: "
# 0. Load previous data
G = commonLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
Grev = formReverseGraph(G)
json_data = open(folderName + repeatFilename, 'r')
repeatList = json.load(json_data)
lenDicCC = commonLib.obtainLength(folderName, contigFilename+"_Double.fasta")
N1 = len(lenDicCC)
print "repeatList: ", repeatList
print "len(G.graphNodesList)", len(G.graphNodesList)
bigDumpList = []
print "len(repeatList)", len(repeatList) , repeatList
for r in repeatList:
rIn, rOut = [], []
for eachitem in r[0]:
rIn.append(eachitem / 2)
for eachitem in r[1]:
rOut.append(eachitem / 2)
if ( len(rIn) == 2 and len(rOut) == 2) or (len(rIn) == 1 and len(rOut) == 1):
print rIn, rOut
if (len(rIn) == 1 and len(rOut) == 1):
rIn = [rIn[0], rIn[0]]
rOut = [rOut[0], rOut[0]]
# 1. Records reachable indices
kkIn , kkOut = [], []
for eachkk in rIn:
kkIn.append(str(eachkk)+"_"+"in")
for eachkk in rOut:
kkOut.append(str(eachkk)+"_"+"out")
markReachableIndices(G, Grev, kkIn, kkOut, N1)
# 2. Marks inside nodes
singleMissList, allPassList = markInsideNodes(G, kkIn, kkOut)
for i in range(4):
print "len(singleMissList[i]), len(allPassList)", len(singleMissList[i]), len(allPassList)
# 3. Finds start/end of repeat
myStartIndex, myEndIndex = markStartEndNodes(G, rIn, rOut, singleMissList, allPassList)
print myStartIndex, myEndIndex
# 4. Find repeat interior by shortest path joining S/E
repeatPathway = markInterior(G , myStartIndex, myEndIndex, N1)
print "repeatPathway", repeatPathway
#checkPathLength(repeatPathway, G, N1, folderName)
# 5. Find flanking region by shortest path search again
flankingPathsList = markFlankingRegion(G, rIn, rOut, myStartIndex, myEndIndex, N1)
print flankingPathsList
# 6. Find associated reads by graph node query
flankingList, repeatList = markAssociatedReads(G, singleMissList, allPassList)
# ## Experimental
repeatList = allPassList
# ## End Experimental
for eachlist in flankingList:
print len(eachlist), len(repeatList)
bigDumpList.append([flankingList, repeatList, repeatPathway, flankingPathsList])
# 7. Format return and move on to the phasing
with open(folderName + repeatSpec, 'w') as outfile:
json.dump(bigDumpList, outfile)
def identifyRepeat(folderName, mummerLink,contigFilename,contigReadGraph, repeatFilename, optionToRun ):
'''
Input : Graph --- phaseStringGraph1
Output: repeat pairs { [ (1,2), (3,4) ] , [(5,6),(7,8)] }
Algorithm:
a) Reachability test on the graph to find the partners
b) Form Bipartite graph
c) Find connected component in the bipartite and define as repeat pairs
'''
# ## (a) reachability test to find partners
G = commonLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
# G.reportEdge()
lenDicCC = commonLib.obtainLength(folderName, contigFilename+"_Double.fasta")
adjacencyList = [[] for i in range(len(lenDicCC))]
N1 = len(lenDicCC)
# # Debug
# for i in range(14):
# debugGraphPath(i, 2, G, N1)
# # End Debug
for i in range(len(lenDicCC)):
adjacencyList[i] = findAllReachable(i, N1, G)
print "i, adjacencyList[i] : ", i , adjacencyList[i]
# ## (b) formation of bipartite graph
if optionToRun == "tandem" :
newAdjacencyList = adjacencyList
elif optionToRun == "xphase":
newAdjacencyList = filterEdge(adjacencyList, folderName, contigFilename)
G2 = commonLib.seqGraph(N1 * 2)
for i in range(N1):
for j in newAdjacencyList[i]:
G2.insertEdge(2 * i, 2 * j + 1, 1)
G2.insertEdge(2 * j + 1, 2 * i, 1)
clusters = G2.findConnectedComponents()
repeatList = []
for eachitem in clusters:
leftList, rightList = [], []
for eachsubitem in eachitem:
if eachsubitem % 2 == 0 :
leftList.append(eachsubitem)
else:
rightList.append(eachsubitem)
repeatList.append([getDistinct(leftList), getDistinct(rightList)])
with open(folderName + repeatFilename, 'w') as outfile:
json.dump(repeatList, outfile)
json_data = open(folderName + repeatFilename, 'r')
loadData = json.load(json_data)
assert(loadData == repeatList)
def formReadContigStringGraph(folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, graphName):
'''
Input : all_associated_reads.fasta, improved3.fasta
Output : (G) String Graph linking the reads and contigs
Algorithm:
a) Form double reads and contigs V
b) Mummer the data and extract dataList three times V
c) Use the subroutine to output a graph V
d) Output the graph to a file phasing_String_graph.graph V
'''
G = []
commonLib.writeToFile_Double1(folderName, contigFilename + ".fasta", contigFilename + "_Double.fasta", "contig")
commonLib.writeToFile_Double1(folderName, readsetFilename + ".fasta", readsetFilename + "_Double.fasta", "reads")
header, referenceFile, queryFile = optTypeFileHeader + "CC", contigFilename + "_Double.fasta" , contigFilename + "_Double.fasta"
if True:
commonLib.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile)
lenDicCC = commonLib.obtainLength(folderName, contigFilename + "_Double.fasta")
dataListCC = commonLib.extractMumData(folderName, header + "Out")
dataListCC = filterData(dataListCC, lenDicCC)
header, referenceFile, queryFile = optTypeFileHeader + "RR", readsetFilename + "_Double.fasta" , readsetFilename + "_Double.fasta"
if True:
commonLib.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile)
lenDicRR = commonLib.obtainLength(folderName, readsetFilename + "_Double.fasta")
dataListRR = commonLib.extractMumData(folderName, header + "Out")
dataListRR = filterData(dataListRR, lenDicRR)
header, referenceFile, queryFile = optTypeFileHeader + "CR", contigFilename + "_Double.fasta" , readsetFilename + "_Double.fasta"
if True:
commonLib.useMummerAlign(mummerLink, folderName, header, referenceFile, queryFile)
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
dataListCR = commonLib.extractMumData(folderName, header + "Out")
dataListCR = filterData(dataListCR, lenDicCR)
numberOfNodes = len(lenDicCR)
G = commonLib.seqGraph(numberOfNodes)
N1, N2 = len(lenDicCC), len(lenDicRR)
print "N1, N2, numberOfNodes: ", N1, N2, numberOfNodes
'''
e.g. of dataListCC[0], dataListRR[0], dataListCR[0]
[1, 520, 2913194, 2913716, 520, 523, 99.05, 'Contig0_d', 'Contig2_d']
[1, 1383, 1253, 2603, 1383, 1351, 82.39, 'Read0_d', 'Read1705_p']
[1, 718, 4334, 5074, 718, 741, 91.91, 'Contig0_d', 'Read1018_d']
'''
# print dataListCC[0]
# print dataListRR[0]
# print dataListCR[0]
# for eachitem in dataListCC:
# print eachitem
addDataToList(dataListCC, G, 0, 0, 'C', 'C')
# for eachitem in dataListRR[0:10]:
# print eachitem , lenDicRR[eachitem[-2]], lenDicRR[eachitem[-1]]
addDataToList(dataListRR, G, N1, N1, 'R', 'R')
addDataToList(dataListCR, G, 0, N1, 'C', 'R')
# G.reportEdge()
G.saveToFile(folderName, graphName)
checkGraphLength(G, N1, lenDicRR)
# print len(G.graphNodesList[0].listOfPrevNodes), len(G.graphNodesList[0].listOfNextNodes)
print "len(G.graphNodesList)", len(G.graphNodesList)
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 = commonLib.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 = commonLib.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)
commonLib.readContigOut(folderName, mummerLink, graphFileName, combinedName, "improved4.fasta", "outOpenListphaing", nameDic)
def defineRepeatAndFlanking(folderName, mummerLink):
'''
Input :
V a) String graph : G
V b) Repeat Pairing : repeatList
Output :
V a) chain of repeat indices (e.g. [S= R1, R33, R45, R24= E])
V b) chain of flanking region indices for in1/2 out1/2 middle (e.g. [C1, R2, R4] )
V c) in1/2 out1/2 and middle reads per repeat (e.g. [R1, R33, R45, R24])
Algorithm :
V 1. Find repeat by graph operations
V 2. Find flanking region by graph operations
V 3. Find associated reads by graph operations
'''
print "defineRepeatAndFlanking: "
# 0. Load previous data
G = commonLib.seqGraph(0)
G.loadFromFile(folderName, "phaseStringGraph1")
Grev = formReverseGraph(G)
json_data = open(folderName + 'phaseRepeat.txt', 'r')
repeatList = json.load(json_data)
lenDicCC = commonLib.obtainLength(folderName, "improved3_Double.fasta")
N1 = len(lenDicCC)
print "repeatList: ", repeatList
print "len(G.graphNodesList)", len(G.graphNodesList)
bigDumpList = []
print "len(repeatList)",len(repeatList) , repeatList
for r in repeatList:
rIn, rOut = [], []
for eachitem in r[0]:
rIn.append(eachitem / 2)
for eachitem in r[1]:
rOut.append(eachitem / 2)
if len(rIn) == 2 and len(rOut) == 2:
print rIn, rOut
# 1. Records reachable indices
kkIn , kkOut = [],[]
'''
for eachnext in G.graphNodesList[4].listOfNextNodes:
print 4, eachnext
kkIn.append(eachnext[0])
for eachprev in G.graphNodesList[6].listOfPrevNodes:
print 6, eachprev
kkOut.append(eachprev[0])
print set(kkIn).intersection(set(kkOut))
print len( G.graphNodesList[0].listOfNextNodes), len( G.graphNodesList[2].listOfNextNodes)
print len( G.graphNodesList[1].listOfPrevNodes), len( G.graphNodesList[3].listOfPrevNodes)
print len( Grev.graphNodesList[0].listOfPrevNodes), len( Grev.graphNodesList[2].listOfPrevNodes)
print len( Grev.graphNodesList[1].listOfNextNodes), len( Grev.graphNodesList[3].listOfNextNodes)
'''
markReachableIndices(G, Grev, rIn, rOut, N1)
# 2. Marks inside nodes
singleMissList, allPassList = markInsideNodes(G, rIn, rOut)
for i in range(4):
print "len(singleMissList[i]), len(allPassList)", len(singleMissList[i]), len(allPassList)
# 3. Finds start/end of repeat
myStartIndex, myEndIndex = markStartEndNodes(G, rIn, rOut, singleMissList, allPassList)
print myStartIndex, myEndIndex
# 4. Find repeat interior by shortest path joining S/E
repeatPathway = markInterior(G , myStartIndex, myEndIndex, N1)
print "repeatPathway", repeatPathway
checkPathLength(repeatPathway, G, N1, folderName)
# 5. Find flanking region by shortest path search again
flankingPathsList = markFlankingRegion(G, rIn, rOut, myStartIndex, myEndIndex, N1)
print flankingPathsList
# 6. Find associated reads by graph node query
flankingList, repeatList = markAssociatedReads(G, singleMissList, allPassList)
### Experimental
repeatList = allPassList
### End Experimental
for eachlist in flankingList:
print len(eachlist), len(repeatList)
bigDumpList.append([flankingList, repeatList, repeatPathway, flankingPathsList])
# 7. Format return and move on to the phasing
with open(folderName + 'repeatSpecification.txt', 'w') as outfile:
json.dump(bigDumpList, outfile)
def resolvingTandem(folderName, mummerPath, contigReadGraph,contigFilename, readsetFilename, optTypeFileHeader, repeatSpec):
print "resolvingTandem"
'''
Input : repeat info
Output : count, join.
Algorithm:
1. Find loops
2. Form repeat
3. Form chain of repeat copies back to back
4. Align reads
5. Calculate extra bases beyond flanking region
6. Calculate count
7. Join the contigs
'''
# 0 ) Load all the data
G = commonLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
lenDicCC = commonLib.obtainLength(folderName, contigFilename+"_Double.fasta")
N1 = len(lenDicCC)
maxDuplicate = 10
repeatTempFilename = "tandemRepeatTemplate.fasta"
mummerFile = "myTandemRepeatTemplate"
myContigsDic = commonLib.loadContigsFromFile(folderName, readsetFilename+"_Double.fasta")
lenDicRR = commonLib.obtainLength(folderName, readsetFilename + "_Double.fasta")
header = optTypeFileHeader + "RR"
dataListRR = commonLib.extractMumData(folderName, header + "Out")
dataListRR = newPhasing.filterData(dataListRR, lenDicRR)
dataListRRDic = {}
for eachitem in dataListRR:
if eachitem[1] > eachitem[3]:
dataListRRDic[eachitem[-2] +";"+eachitem[-1]] = eachitem[4]
header = optTypeFileHeader + "CR"
lenDicCC = commonLib.obtainLength(folderName, contigFilename + "_Double.fasta")
lenDicCR = dict(lenDicCC.items() + lenDicRR.items())
dataListCR = commonLib.extractMumData(folderName, header + "Out")
dataListCR = newPhasing.filterData(dataListCR, lenDicCR)
dataListCRDic = {}
for eachitem in dataListCR:
if eachitem[1] > eachitem[3]:
dataListCRDic[eachitem[-2] +";"+eachitem[-1]] = eachitem[4]
print dataListCRDic
json_data = open(folderName + repeatSpec, 'r')
loadData = json.load(json_data)
contigsTmp = commonLib.loadContigsFromFile(folderName, contigFilename+"_Double.fasta")
readTmp = commonLib.loadContigsFromFile(folderName, readsetFilename + "_Double.fasta")
happyTandemList = {}
for eachrepProfile in loadData:
# 1)
startContig = eachrepProfile[-1][0][0]
isTerminate, returnPathList = DFSwithPath(G, G.graphNodesList[startContig], [startContig], N1, False)
# 2)
if isTerminate:
v = returnPathList[-1]
i =0
tandemPath = []
while i < len(returnPathList):
if returnPathList[i] == v:
tandemPath = returnPathList[i:]
i = len(returnPathList)
i = i +1
print returnPathList
print tandemPath
# 3) [fix it when have time later ; to just use graph; bug at the min thing]
repeatContent = ""
for kk in range(len(tandemPath[0:-1])):
eachitem = tandemPath[kk]- N1
nextitem = tandemPath[kk+1] - N1
readName = "Read" + str(eachitem/2) + "_"
nextReadName = "Read" + str(nextitem/2) + "_"
if eachitem %2 ==0 :
readName = readName + "p"
elif eachitem %2 ==1:
readName = readName + "d"
if nextitem %2 ==0 :
nextReadName = nextReadName + "p"
elif nextitem %2 ==1:
nextReadName = nextReadName + "d"
overlap = dataListRRDic[readName + ";" + nextReadName]
print overlap
repeatContent = repeatContent + myContigsDic[readName][0:-overlap]
print "len(repeatContent)", len(repeatContent)
fout = open(folderName + repeatTempFilename, 'w')
fout.write(">RepeatSegment\n")
repeatContentLarge = ""
for i in range(maxDuplicate):
fout.write(repeatContent)
repeatContentLarge= repeatContentLarge + repeatContent
fout.close()
# 4)
repeatReadList = eachrepProfile[1]
myList= []
for eachitem in repeatReadList:
readName = "Read" + str((eachitem- N1)/2) + "_"
if eachitem %2 ==0 :
readName = readName + "p"
elif eachitem %2 ==1:
readName = readName + "d"
myList.append(readName)
commonLib.putListToFileO(folderName, readsetFilename+"_Double.fasta", "toAlignReads", myList)
if True:
commonLib.useMummerAlign(mummerPath, folderName,mummerFile , repeatTempFilename, "toAlignReads.fasta")
dataList = commonLib.extractMumData(folderName, mummerFile+"Out")
# 5)
totalBasesMatch = 0
lrepeat = len(repeatContent)
c = 50 # Important parameters : FIX needed in production
#lengthDic = commonLib.obtainLength(folderName, readsetFilename+"_Double.fasta")
print "dataList[0]", dataList[0]
dataList.sort(key = itemgetter(-1))
for key, values in groupby(dataList,itemgetter(-1)):
maxValue = -1
for eachsub in values:
if eachsub[5] > maxValue:
maxValue = eachsub[5]
#print key, maxValue
totalBasesMatch = totalBasesMatch + maxValue
print c, lrepeat, totalBasesMatch
ct = totalBasesMatch*1.0/(c*lrepeat)
print "BIG NUMBER of THE DAY: ", ct
# 6)
# a) find the starting point
startContig = eachrepProfile[-1][0][0]
firstRead = eachrepProfile[-1][0][1]-N1
contigName = "Contig"+ str(startContig/2)
if startContig %2 == 0:
contigName = contigName + "_p"
elif startContig%2 ==1:
contigName = contigName + "_d"
readName = "Read"+ str(firstRead/2)
if firstRead %2 == 0:
readName = readName + "_p"
elif firstRead%2 ==1:
readName = readName + "_d"
overlapFirst = dataListCRDic[contigName+";"+readName]
tmpCombine = contigsTmp[contigName][0:-overlapFirst] + readTmp[readName]
f1 = open(folderName + "firstOverlap.fasta", 'w')
f1.write(">combined\n")
f1.write(tmpCombine)
f1.close()
if True:
commonLib.useMummerAlign(mummerPath, folderName,"myFirstOverlap" , repeatTempFilename, "firstOverlap.fasta")
dataList = commonLib.extractMumData(folderName, "myFirstOverlap"+"Out")
dataList.sort(key = itemgetter(0))
maxVal = -1
maxItm = []
for eachi in dataList:
if eachi[5] > maxVal:
maxVal = eachi[5]
maxItm = eachi
print maxItm
repeatStart = maxItm[0]
contigEnd = maxItm[2]
# b) format return : prepare the repeat template
print "ct*lrepeat", int(repeatStart + ct*lrepeat)
print "repeatStart", repeatStart
happyTandemList[contigName]= repeatContentLarge[repeatStart:int(repeatStart + ct*lrepeat)]
contigsTmp[contigName] = tmpCombine[0:contigEnd]
print "len(contigsTmp[contigName])", len(contigsTmp[contigName])
print "len(happyTandemList[contigName])", len(happyTandemList[contigName])
# 7) Combine all the repeat information and do the join
leaderList = [i for i in range(len(contigsTmp))]
for eachrepProfile in loadData:
startContig = eachrepProfile[-1][0][0]
endContig = eachrepProfile[-1][-1][-1]
leaderContig = leaderList[startContig]
leaderName = parseIDToName(leaderContig)
endName = parseIDToName(endContig)
startName = parseIDToName(startContig)
contigsTmp[leaderName] = contigsTmp[leaderName] + happyTandemList[startName]
if endContig != leaderContig:
contigsTmp[leaderName] = contigsTmp[leaderName] + contigsTmp[endName]
contigsTmp[endName] = ""
leaderList[endContig] = leaderContig
leaderAgg = [[] for i in range(len(leaderList))]
for i in range(len(leaderList)):
leaderAgg[leaderList[i]].append(i)
checkingList = [False for i in range(N1)]
fout = open(folderName + "tademResolved.fasta", 'w')
counter = 0
for eachcontig in contigsTmp:
id = newPhasing.parseEdgeNameToID(eachcontig, 'C')
if checkingList[id/2] == False:
fout.write(">Segkk"+str(counter)+ "\n")
fout.write(contigsTmp[eachcontig])
counter = counter + 1
for eachkk in leaderAgg[leaderList[id]]:
checkingList[eachkk/2] = True
fout.close()
