def formResolveListForMatch(folderName, newInList, newOutList, sd, contigReadGraph, N1):
resolvedList = []
for eachitem in newInList:
found = satisfyMatch(eachitem, newOutList, sd)
if found != -1:
leftCtgIndex, rightCtgIndex = eachitem[0], found
succReadsList = abunGraphLib.findPathBtwEnds(folderName, leftCtgIndex, rightCtgIndex, contigReadGraph, N1)
if succReadsList != None:
resolvedList.append([eachitem[0], found])
return resolvedList
def formResolveListForMatch(folderName, newInList, newOutList, sd,
contigReadGraph, N1):
resolvedList = []
for eachitem in newInList:
found = satisfyMatch(eachitem, newOutList, sd)
if found != -1:
leftCtgIndex, rightCtgIndex = eachitem[0], found
succReadsList = abunGraphLib.findPathBtwEnds(
folderName, leftCtgIndex, rightCtgIndex, contigReadGraph, N1)
if succReadsList != None:
resolvedList.append([eachitem[0], found])
return resolvedList
def xNodeResolving(folderName, contigReadGraph):
### Init G, myCountDic, N1
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
with open(folderName + "myCountDic.json") as f:
myCountDic = json.load(f)
N1 = len(myCountDic) * 2
### Add resolved edge
adj = [[] for i in range(N1)]
for i in range(N1):
adj[i] = abunGraphLib.findAllReachable(i, N1, G)
Gnew = graphLib.seqGraph(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i, j, 1)
extraCounter = 0
mapDummyToRealDic = {}
resolvedList = []
for v in Gnew.graphNodesList:
inList = []
for eachitem in v.listOfPrevNodes:
inList.append(eachitem[0])
outList = []
for eachitem in v.listOfNextNodes:
outList.append(eachitem[0])
inListCt = getCtTwoToOne(inList, myCountDic)
outListCt = getCtTwoToOne(outList, myCountDic)
sizeList = []
for eachitem in myCountDic:
sizeList.append(myCountDic[eachitem])
sd = np.std(sizeList)
for eachIn in inListCt:
matchedOut = satisfyMatch(eachIn, outListCt, sd)
if matchedOut != -1:
leftCtgIndex, rightCtgIndex = eachIn[0], v.nodeIndex
inSuccReadsList = abunGraphLib.findPathBtwEnds(
folderName, leftCtgIndex, rightCtgIndex, contigReadGraph, N1
)
leftCtgIndex, rightCtgIndex = v.nodeIndex, matchedOut
outSuccReadsList = abunGraphLib.findPathBtwEnds(
folderName, leftCtgIndex, rightCtgIndex, contigReadGraph, N1
)
if inSuccReadsList != None and outSuccReadsList != None:
resolvedList.append([eachIn[0]] + inSuccReadsList + [N1 + extraCounter])
print "in: ", resolvedList[-1]
resolvedList.append([N1 + extraCounter] + outSuccReadsList + [matchedOut])
print "out: ", resolvedList[-1]
mapDummyToRealDic[extraCounter] = v.nodeIndex
extraCounter = extraCounter + 1
return resolvedList, mapDummyToRealDic
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]
def xNodeResolving(folderName, contigReadGraph):
'''
Input : contigGraph , abunInfo , folderName
Output: myresolvedList.json, gapContentLookUp.json, dummyNodeMapping.json
Algorithm :
1) Tranverse the graph
a) If the node can well be fixed with sd requirement met
i) Link it across and add the pair into the myresolvedList, gapContentLookUp
ii) Add dummynodes and fill in the dummyNodeMapping
2) Format return and output as temp file
'''
### Init G, myCountDic, N1
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
with open(folderName + 'myCountDic.json') as f:
myCountDic = json.load(f)
N1 = len(myCountDic) * 2
### Add resolved edge
adj = [[] for i in range(N1)]
for i in range(N1):
adj[i] = abunGraphLib.findAllReachable(i, N1, G)
Gnew = graphLib.seqGraph(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i, j, 1)
extraCounter = 0
mapDummyToRealDic = {}
resolvedList = []
for v in Gnew.graphNodesList:
inList = []
for eachitem in v.listOfPrevNodes:
inList.append(eachitem[0])
outList = []
for eachitem in v.listOfNextNodes:
outList.append(eachitem[0])
inListCt = getCtTwoToOne(inList, myCountDic)
outListCt = getCtTwoToOne(outList, myCountDic)
sizeList = []
for eachitem in myCountDic:
sizeList.append(myCountDic[eachitem])
sd = np.std(sizeList)
for eachIn in inListCt:
matchedOut = satisfyMatch(eachIn, outListCt, sd)
if matchedOut != -1:
leftCtgIndex, rightCtgIndex = eachIn[0], v.nodeIndex
inSuccReadsList = abunGraphLib.findPathBtwEnds(
folderName, leftCtgIndex, rightCtgIndex, contigReadGraph,
N1)
leftCtgIndex, rightCtgIndex = v.nodeIndex, matchedOut
outSuccReadsList = abunGraphLib.findPathBtwEnds(
folderName, leftCtgIndex, rightCtgIndex, contigReadGraph,
N1)
if inSuccReadsList != None and outSuccReadsList != None:
resolvedList.append([eachIn[0]] + inSuccReadsList +
[N1 + extraCounter])
print "in: ", resolvedList[-1]
resolvedList.append([N1 + extraCounter] +
outSuccReadsList + [matchedOut])
print "out: ", resolvedList[-1]
mapDummyToRealDic[extraCounter] = v.nodeIndex
extraCounter = extraCounter + 1
return resolvedList, mapDummyToRealDic
