def condenseEdgeRemove(self, G_ContigRead, folderName, mummerLink, contigFilename):
print "condenseEdgeRemove"
thresPass = 100
thresForStrangeCut = 5000
### kkdebug
toRemoveList = []
for eachnode in self.graphNodesList:
if len(eachnode.nodeIndexList) > 0:
if len(eachnode.listOfNextNodes) ==1 :
nextNodeIndex = eachnode.listOfNextNodes[0][0]
nextNode= self.graphNodesList[nextNodeIndex]
if len(nextNode.listOfPrevNodes) == 1 :
currentName = eachnode.nodeIndex
nextName = nextNode.nodeIndex
contigReadPaths = findAllPathK(currentName,nextName, G_ContigRead, 5)
cName = abunHouseKeeper.parseIDToName(currentName,'C',0)
nName = abunHouseKeeper.parseIDToName(nextName,'C',0)
noGoNext = self.readInJSON(folderName, "noGoNext.json")
noGoPrev = self.readInJSON(folderName, "noGoPrev.json")
overlap = [-1, -1]
ctr = 0
for eachpath in contigReadPaths:
if len(eachpath) > 2:
ctr = ctr + 1
elif len(eachpath) == 2:
contigName = cName
leftSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
contigName = nName
rightSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
overlap = IORobot.align(leftSeg, rightSeg, folderName, mummerLink)
if ctr <= thresPass and (cName in noGoNext or nName in noGoPrev or overlap[0] > thresForStrangeCut ):
self.removeEdge(currentName, nextName)
toRemoveList.append([currentName, nextName])
### kkdebug
#with open( "dataFolder/toRemoveList.json", 'w') as f:
# json.dump(toRemoveList, f)
self.findAdjList()
def condenseEdgeRemove(self, G_ContigRead, folderName, mummerLink, contigFilename):
print "condenseEdgeRemove"
thresPass = 100
thresForStrangeCut = 5000
### kkdebug
toRemoveList = []
for eachnode in self.graphNodesList:
if len(eachnode.nodeIndexList) > 0:
if len(eachnode.listOfNextNodes) ==1 :
nextNodeIndex = eachnode.listOfNextNodes[0][0]
nextNode= self.graphNodesList[nextNodeIndex]
if len(nextNode.listOfPrevNodes) == 1 :
currentName = eachnode.nodeIndex
nextName = nextNode.nodeIndex
contigReadPaths = findAllPathK(currentName,nextName, G_ContigRead, 5)
cName = abunHouseKeeper.parseIDToName(currentName,'C',0)
nName = abunHouseKeeper.parseIDToName(nextName,'C',0)
noGoNext = self.readInJSON(folderName, "noGoNext.json")
noGoPrev = self.readInJSON(folderName, "noGoPrev.json")
overlap = [-1, -1]
ctr = 0
for eachpath in contigReadPaths:
if len(eachpath) > 2:
ctr = ctr + 1
elif len(eachpath) == 2:
contigName = cName
leftSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
contigName = nName
rightSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
overlap = IORobot.align(leftSeg, rightSeg, folderName, mummerLink)
if ctr <= thresPass and (cName in noGoNext or nName in noGoPrev or overlap[0] > thresForStrangeCut ):
self.removeEdge(currentName, nextName)
toRemoveList.append([currentName, nextName])
### kkdebug
#with open( "dataFolder/toRemoveList.json", 'w') as f:
# json.dump(toRemoveList, f)
self.findAdjList()
def singleGapLookUp(eachmatchpair,folderName, N1, mummerLink, contigReadGraph, contigFilename,readsetFilename):
#print eachmatchpair
leftCtgIndex ,rightCtgIndex, leftEnd, rightStart, middleContent = eachmatchpair[0],eachmatchpair[-1],0,0,""
succReadsList = []
G = seqGraphWt(0)
G.loadFromFile(folderName, contigReadGraph)
succReadsList = BFS(leftCtgIndex,rightCtgIndex, G, N1)
if len(succReadsList) > 0:
succReadsList.pop(0)
succReadsList.pop(-1)
else:
print "interesting item for future study"
print "succReadsList" , succReadsList
if len(succReadsList) == 0:
contigName = abunHouseKeeper.parseIDToName(leftCtgIndex, 'C', N1)
leftSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
contigName = abunHouseKeeper.parseIDToName(rightCtgIndex, 'C', N1)
rightSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
overlap = IORobot.alignWithName(leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex) )
print "overlap contig : ", overlap
leftEnd = len(leftSeg) - overlap[0]
middleContent = ""
else:
contigName = abunHouseKeeper.parseIDToName(leftCtgIndex, 'C', N1)
print contigName
leftSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
readName = abunHouseKeeper.parseIDToName(succReadsList[0], 'R', N1)
print readName
rightSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
overlap = IORobot.alignWithName(leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex) )
print "overlap start read : ", overlap
leftEnd = len(leftSeg) - overlap[0]
middleContent = ""
for i in range(len(succReadsList)-1):
readName = abunHouseKeeper.parseIDToName(succReadsList[i], 'R', N1)
leftSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
readName = abunHouseKeeper.parseIDToName(succReadsList[i+1], 'R', N1)
rightSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
overlap = IORobot.alignWithName(leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex) )
print "overlap middle read : ", overlap
middleContent = middleContent + leftSeg[0:len(leftSeg)-overlap[0]]
readName = abunHouseKeeper.parseIDToName(succReadsList[-1], 'R', N1)
leftSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
contigName = abunHouseKeeper.parseIDToName(rightCtgIndex, 'C', N1)
rightSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
overlap = IORobot.alignWithName(leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex) )
print "overlap end read : ", overlap
middleContent = middleContent + leftSeg[0:len(leftSeg)-overlap[0]]
return [leftCtgIndex ,rightCtgIndex, leftEnd, rightStart, middleContent]
def singleGapLookUp(eachmatchpair, folderName, N1, mummerLink, contigReadGraph, contigFilename, readsetFilename):
print eachmatchpair
leftCtgIndex, rightCtgIndex, leftEnd, rightStart, middleContent = eachmatchpair[0], eachmatchpair[-1], 0, 0, ""
succReadsList = abunGraphLib.findPathBtwEnds(folderName, leftCtgIndex, rightCtgIndex, contigReadGraph, N1)
succReadsList = []
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
allPaths = abunGraphLib.findAllPathK(leftCtgIndex, rightCtgIndex, G, 5)
# shuffle(allPaths)
print "allPaths", allPaths
possibleList = []
for p in allPaths:
noContig = True
for pp in p[1:-1]:
if pp < N1:
noContig = False
if noContig == True:
possibleList.append(p)
print "possibleList", possibleList
minListLen = 1000
for p in possibleList:
if len(p) < minListLen:
succReadsList = p
minListLen = len(p)
if len(succReadsList) > 0:
succReadsList.pop(0)
succReadsList.pop(-1)
else:
print "interesting item for future study"
print "succReadsList", succReadsList
if len(succReadsList) == 0:
contigName = abunHouseKeeper.parseIDToName(leftCtgIndex, "C", N1)
leftSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
contigName = abunHouseKeeper.parseIDToName(rightCtgIndex, "C", N1)
rightSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
overlap = IORobot.alignWithName(
leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex)
)
print "overlap contig : ", overlap
leftEnd = len(leftSeg) - overlap[0]
middleContent = ""
else:
contigName = abunHouseKeeper.parseIDToName(leftCtgIndex, "C", N1)
print contigName
leftSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
readName = abunHouseKeeper.parseIDToName(succReadsList[0], "R", N1)
print readName
rightSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
overlap = IORobot.alignWithName(
leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex)
)
print "overlap start read : ", overlap
leftEnd = len(leftSeg) - overlap[0]
middleContent = ""
for i in range(len(succReadsList) - 1):
readName = abunHouseKeeper.parseIDToName(succReadsList[i], "R", N1)
leftSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
readName = abunHouseKeeper.parseIDToName(succReadsList[i + 1], "R", N1)
rightSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
overlap = IORobot.alignWithName(
leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex)
)
print "overlap middle read : ", overlap
middleContent = middleContent + leftSeg[0 : len(leftSeg) - overlap[0]]
readName = abunHouseKeeper.parseIDToName(succReadsList[-1], "R", N1)
leftSeg = IORobot.myRead(folderName, readsetFilename + "_Double.fasta", readName)
contigName = abunHouseKeeper.parseIDToName(rightCtgIndex, "C", N1)
rightSeg = IORobot.myRead(folderName, contigFilename + "_Double.fasta", contigName)
overlap = IORobot.alignWithName(
leftSeg, rightSeg, folderName, mummerLink, str(leftCtgIndex) + "_" + str(rightCtgIndex)
)
print "overlap end read : ", overlap
middleContent = middleContent + leftSeg[0 : len(leftSeg) - overlap[0]]
return [leftCtgIndex, rightCtgIndex, leftEnd, rightStart, middleContent]