def formConfirmReadResolve(folderName, inList, outList, G, Grev, N1):
#print "formConfirmReadResolve"
resolvedList = []
confirmingReadList = []
brLFlankList = []
brRFlankList = []
### Find possible candidate reads
print "inList , outList formConfirmReadResolve()", inList, outList
for eachin in inList:
for eachout in outList:
pathList = abunGraphLib.findAllPathK(eachin, eachout, G, 3)
for path in pathList:
if len(path) == 3 and path[1] >= N1:
R = path[1]
confirmingReadList.append(R)
brLFlankList.append([eachin, R])
brRFlankList.append([eachout, R])
### Filter simple false cases
toUseReadDic = {}
confirmingReadList.sort()
for key, items in groupby(confirmingReadList):
toUseReadDic[str(key)] = True
newbrLFlankList = abunHouseKeeper.getDistinct(brLFlankList)
newbrLFlankList.sort(key=itemgetter(1))
for key, items in groupby(newbrLFlankList, itemgetter(1)):
mylist = list(items)
if len(mylist) > 1:
toUseReadDic[str(key)] = False
newbrRFlankList = abunHouseKeeper.getDistinct(brRFlankList)
newbrRFlankList.sort(key=itemgetter(1))
for key, items in groupby(newbrRFlankList, itemgetter(1)):
mylist = list(items)
if len(mylist) > 1:
toUseReadDic[str(key)] = False
finalSearchReadList = []
for eachitem in toUseReadDic:
if toUseReadDic[eachitem] == True:
finalSearchReadList.append(int(eachitem))
### Check paths to confirm all false cases
for eachR in finalSearchReadList:
l1 = abunGraphLib.findAllReachable(eachR, N1, G)
l2 = abunGraphLib.findAllReachable(eachR, N1, Grev)
l1Distinct = abunHouseKeeper.getDistinct(l1)
l2Distinct = abunHouseKeeper.getDistinct(l2)
if len(l1Distinct) == 1 and len(l2Distinct) == 1:
c1, c2 = l1Distinct[0], l2Distinct[0]
resolvedList.append([c2, c1])
return resolvedList
def graphSurgery(myCountDic, folderName, contigReadGraph, mummerLink, readsetFilename, contigFilename):
### Transitive reduction and remove double pointers
N1 = len(myCountDic) * 2
print "N1", N1
kthres = abunHouseKeeper.abunGlobalSplitParameterRobot.kthres
edgeThres = abunHouseKeeper.abunGlobalSplitParameterRobot.edgeThres
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
adj = [[] for i in range(N1)]
for i in range(N1):
tmpList = abunGraphLib.findAllReachable(i, N1, G)
for j in tmpList:
if len(abunGraphLib.findAllPathK(i, j, G, kthres)) >= edgeThres:
adj[i].append(j)
### Filter adaptor skipped case
adaptorPair = []
for i in range(len(adj)):
if i % 2 == 0:
if i + 1 in adj[i]:
adj[i].remove(i + 1)
adaptorPair.append([i, i + 1])
elif i % 2 == 1:
if i - 1 in adj[i]:
adj[i].remove(i - 1)
adaptorPair.append([i, i - 1])
Gnew = abunGraphLib.seqGraphDynamic(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i, j, 1997)
for eachpair in adaptorPair:
u, v = eachpair[0], eachpair[1]
for x in Gnew.graphNodesList[u].listOfPrevNodes:
xIndex = x[0]
Gnew.removeEdge(xIndex, v)
for y in Gnew.graphNodesList[v].listOfNextNodes:
yIndex = y[0]
Gnew.removeEdge(u, yIndex)
### Trying out the new component
import toCondenseFixer
Gnew = toCondenseFixer.noGoZoneDefiner(Gnew, folderName)
Gnew.symGraph()
### End filter adaptor skipped case
if abunHouseKeeper.abunGlobalSplitParameterRobot.runGraphSurgery:
Gnew.initAdv()
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunCondenseRemove:
Gnew.condenseEdgeRemove(G, folderName, mummerLink, contigFilename)
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunDoubltPtr:
Gnew.doubleEdgeReduction()
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunTransitive:
Gnew.transitiveReduction(
folderName, mummerLink, contigFilename + "_Double.fasta", readsetFilename + "_Double.fasta", G
)
Gnew.condense()
Gnew.findAdjList()
else:
Gnew.initAdv()
Gnew.condense()
Gnew.findAdjList()
return Gnew
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 formConfirmReadResolve(folderName, inList, outList, G, Grev, N1):
# print "formConfirmReadResolve"
resolvedList = []
confirmingReadList = []
brLFlankList = []
brRFlankList = []
### Find possible candidate reads
print "inList , outList formConfirmReadResolve()", inList, outList
for eachin in inList:
for eachout in outList:
pathList = abunGraphLib.findAllPathK(eachin, eachout, G, 3)
for path in pathList:
if len(path) == 3 and path[1] >= N1:
R = path[1]
confirmingReadList.append(R)
brLFlankList.append([eachin, R])
brRFlankList.append([eachout, R])
### Filter simple false cases
toUseReadDic = {}
confirmingReadList.sort()
for key, items in groupby(confirmingReadList):
toUseReadDic[str(key)] = True
newbrLFlankList = abunHouseKeeper.getDistinct(brLFlankList)
newbrLFlankList.sort(key=itemgetter(1))
for key, items in groupby(newbrLFlankList, itemgetter(1)):
mylist = list(items)
if len(mylist) > 1:
toUseReadDic[str(key)] = False
newbrRFlankList = abunHouseKeeper.getDistinct(brRFlankList)
newbrRFlankList.sort(key=itemgetter(1))
for key, items in groupby(newbrRFlankList, itemgetter(1)):
mylist = list(items)
if len(mylist) > 1:
toUseReadDic[str(key)] = False
finalSearchReadList = []
for eachitem in toUseReadDic:
if toUseReadDic[eachitem] == True:
finalSearchReadList.append(int(eachitem))
### Check paths to confirm all false cases
for eachR in finalSearchReadList:
l1 = abunGraphLib.findAllReachable(eachR, N1, G)
l2 = abunGraphLib.findAllReachable(eachR, N1, Grev)
l1Distinct = abunHouseKeeper.getDistinct(l1)
l2Distinct = abunHouseKeeper.getDistinct(l2)
if len(l1Distinct) == 1 and len(l2Distinct) == 1:
c1, c2 = l1Distinct[0], l2Distinct[0]
resolvedList.append([c2, c1])
return resolvedList
def continuousIntegration():
if False:
G = graphLib.seqGraph(10)
for i in range(5):
G.insertEdge(i,i+1,1997)
G.insertEdge(i,i+2, 1997)
resultList = abunGraphLib.BFS_revisit(1,3,G,1)
print "resultList", resultList
if False :
folderName, mummerPath, directPathList, indirectPathList, contigFile, readFile = \
"Apr10Test/", "/usr/bin/", [[1, 486, 217], [1, 8642, 217], [1, 13465, 217]], [[1, 486, 217]], "improved3_Double.fasta", "phasingSeedName_Double.fasta"
abunGraphLib.formPathSeq(folderName, mummerPath, directPathList, indirectPathList, contigFile, readFile)
if False:
lenDic = IORobot.obtainLength(folderName , contigFile)
N1 = len(lenDic)
print "N1", N1
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, "phaseStringGraph1")
adj = [[] for i in range(N1)]
for i in range(N1):
adj[i] = abunGraphLib.findAllReachable(i, N1, G)
Gnew = abunGraphLib.seqGraphDynamic(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i,j,1997)
Gnew.initAdv()
Gnew.doubleEdgeReduction()
contigPaths = abunGraphLib.findAllPathK(1, 217, Gnew, 3)
contigReadPaths = abunGraphLib.findAllPathK(1, 217, G, 5)
print "contigPaths", contigPaths
print "contigReadPaths", contigReadPaths
Gnew.transitiveReduction()
if False:
toDelete = abunGraphLib.decideCut("Apr10Test/", "/usr/bin/")
print toDelete
if False:
G = graphLib.seqGraph(0)
G.loadFromFile("Apr10TestA/", "xResolvedGraph")
if False:
for i in range(len(G.graphNodesList)):
v = G.graphNodesList[i]
if len(v.nodeIndexList) > 0:
print i , v.listOfPrevNodes , v.listOfNextNodes
G.reportEdge()
lenDic = IORobot.obtainLength("Apr10TestA/", "improved3_Double.fasta")
mylist = [401, 207, 405, 407, 344]
json_data = open("Apr10TestA/" + "myCountDic.json", 'r')
myCountDic = json.load(json_data)
for x in mylist:
print x, lenDic["Contig"+str(x/2)+"_p"], myCountDic["Segkk"+str(x/2)]
if False:
folderName = "Apr10TestA/"
G = graphLib.seqGraph(0)
G.loadFromFile(folderName , "xResolvedGraph")
json_data = open(folderName + "mapDummyToRealDic.json", 'r')
mapDummyToRealDic = json.load(json_data)
lenDic = IORobot.obtainLength(folderName, "improved3_Double.fasta")
print len(G.graphNodesList)
print len(mapDummyToRealDic)
print "fake N1 , real N1 ", len(G.graphNodesList) - len(mapDummyToRealDic), len(lenDic)
if False:
abunSplitter.mainFlow("Apr10TestB/", "/usr/bin/")
if False:
nonRedundantResolver.removeEmbedded("Apr10TestD/", "/usr/bin/")
if False:
folderName, contigReadGraph = "Apr10TestA/", "phaseStringGraph1"
G = graphLib.seqGraph(0)
kthres, edgeThres = 3, 1
G.loadFromFile(folderName, contigReadGraph)
lenDic = IORobot.obtainLength(folderName , "improved3_Double.fasta")
N1 = len(lenDic)
adj = [[] for i in range(N1)]
for i in range(N1):
tmpList = abunGraphLib.findAllReachable(i, N1, G)
for j in tmpList:
if len(abunGraphLib.findAllPathK(i,j,G,kthres)) >= edgeThres:
adj[i].append(j)
#print i, adj[i]
### Filter adaptor skipped case
adaptorPair = []
for i in range(len(adj)):
if i % 2 == 0:
if i + 1 in adj[i]:
adj[i].remove(i+1)
adaptorPair.append([i, i+1])
elif i % 2 ==1:
if i-1 in adj[i] :
adj[i].remove(i-1)
adaptorPair.append([i, i-1])
Gnew = abunGraphLib.seqGraphDynamic(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i,j,1997)
for eachpair in adaptorPair:
u, v = eachpair[0], eachpair[1]
for x in Gnew.graphNodesList[u].listOfPrevNodes:
xIndex = x[0]
Gnew.removeEdge(xIndex, v)
for y in Gnew.graphNodesList[v].listOfNextNodes:
yIndex = y[0]
Gnew.removeEdge(u, yIndex)
#Gnew.reportEdge()
count2 = 0
for i in range(len(Gnew.graphNodesList)):
if len(Gnew.graphNodesList[i].listOfPrevNodes) == 2 and len(Gnew.graphNodesList[i].listOfNextNodes) == 2:
count2 = count2 + 1
print str(i)+"{color:red}"
print "count2, ", count2
### End filter adaptor skipped case
if True:
nonRedundantResolver.removeRedundantWithFile("May11TestB/" , "/usr/bin/", "abun", "abunDebug", "abunNoEmbed")
def graphSurgery(myCountDic, folderName, contigReadGraph, mummerLink,
readsetFilename, contigFilename):
### Transitive reduction and remove double pointers
N1 = len(myCountDic) * 2
print "N1", N1
kthres = abunHouseKeeper.abunGlobalSplitParameterRobot.kthres
edgeThres = abunHouseKeeper.abunGlobalSplitParameterRobot.edgeThres
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
adj = [[] for i in range(N1)]
for i in range(N1):
tmpList = abunGraphLib.findAllReachable(i, N1, G)
for j in tmpList:
if len(abunGraphLib.findAllPathK(i, j, G, kthres)) >= edgeThres:
adj[i].append(j)
### Filter adaptor skipped case
adaptorPair = []
for i in range(len(adj)):
if i % 2 == 0:
if i + 1 in adj[i]:
adj[i].remove(i + 1)
adaptorPair.append([i, i + 1])
elif i % 2 == 1:
if i - 1 in adj[i]:
adj[i].remove(i - 1)
adaptorPair.append([i, i - 1])
Gnew = abunGraphLib.seqGraphDynamic(N1)
for i in range(N1):
for j in adj[i]:
Gnew.insertEdge(i, j, 1997)
for eachpair in adaptorPair:
u, v = eachpair[0], eachpair[1]
for x in Gnew.graphNodesList[u].listOfPrevNodes:
xIndex = x[0]
Gnew.removeEdge(xIndex, v)
for y in Gnew.graphNodesList[v].listOfNextNodes:
yIndex = y[0]
Gnew.removeEdge(u, yIndex)
Gnew.reportEdge()
### Trying out the new component
import toCondenseFixer
Gnew = toCondenseFixer.noGoZoneDefiner(Gnew, folderName)
Gnew.symGraph()
#Gnew.reportEdge()
### End filter adaptor skipped case
if abunHouseKeeper.abunGlobalSplitParameterRobot.runGraphSurgery:
Gnew.initAdv()
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunCondenseRemove:
Gnew.condenseEdgeRemove(G, folderName, mummerLink, contigFilename)
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunDoubltPtr:
Gnew.doubleEdgeReduction()
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunTransitive:
Gnew.transitiveReduction(folderName, mummerLink,
contigFilename + "_Double.fasta",
readsetFilename + "_Double.fasta", G)
Gnew.condense()
Gnew.findAdjList()
else:
Gnew.initAdv()
Gnew.condense()
Gnew.findAdjList()
return Gnew
