def XResolution(folderName, contigReadGraph, Gnew, myCountDic, lenDic, N1,
mummerLink):
if abunHouseKeeper.abunGlobalSplitParameterRobot.runXResolve:
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
Grev = abunGraphLib.formReverseGraphFast(G)
if not abunHouseKeeper.abunGlobalRunEM:
xResolvedList, brResolvedListforX = [[] for i in range(N1)
], [[] for i in range(N1)]
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunAbunX:
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerX > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLower = abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerX
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperX > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpper = abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperX
xResolvedList = xNodeAdvResolving(Gnew, G, folderName,
myCountDic, lenDic)
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunBRX:
if abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresX > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThres = abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresX
brResolvedListforX = xNodeBrResolving(Gnew, G, Grev,
folderName, N1)
combinedList = resolveConflictX(xResolvedList, brResolvedListforX)
else:
combinedList = xNodeEMResolving(Gnew, G, Grev, folderName,
myCountDic, lenDic, N1, mummerLink)
print "combinedList", combinedList
Gnew.xResolve(combinedList)
Gnew.condense()
Gnew.saveToFile(folderName, "xResolvedGraph")
with open(folderName + "mapDummyToRealDic.json", 'w') as f:
json.dump(Gnew.mapDummyToRealDic, f)
with open(folderName + "xResolvedSimplifiedList.json", 'w') as f:
json.dump(Gnew.xResolvedSimplifiedList, f)
else:
Gnew.saveToFile(folderName, "xResolvedGraph")
with open(folderName + "mapDummyToRealDic.json", 'w') as f:
json.dump(Gnew.mapDummyToRealDic, f)
with open(folderName + "xResolvedSimplifiedList.json", 'w') as f:
json.dump(Gnew.xResolvedSimplifiedList, f)
def XResolution(folderName, contigReadGraph, Gnew, myCountDic, lenDic, N1):
if abunHouseKeeper.abunGlobalSplitParameterRobot.runXResolve:
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
Grev = abunGraphLib.formReverseGraphFast(G)
xResolvedList, brResolvedListforX = [[] for i in range(N1)], [[] for i in range(N1)]
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunAbunX:
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerX > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLower = (
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerX
)
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperX > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpper = (
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperX
)
xResolvedList = xNodeAdvResolving(Gnew, G, folderName, myCountDic, lenDic)
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunBRX:
if abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresX > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThres = (
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresX
)
brResolvedListforX = xNodeBrResolving(Gnew, G, Grev, folderName, N1)
combinedList = resolveConflictX(xResolvedList, brResolvedListforX)
Gnew.xResolve(combinedList)
Gnew.condense()
Gnew.saveToFile(folderName, "xResolvedGraph")
with open(folderName + "mapDummyToRealDic.json", "w") as f:
json.dump(Gnew.mapDummyToRealDic, f)
with open(folderName + "xResolvedSimplifiedList.json", "w") as f:
json.dump(Gnew.xResolvedSimplifiedList, f)
else:
Gnew.saveToFile(folderName, "xResolvedGraph")
with open(folderName + "mapDummyToRealDic.json", "w") as f:
json.dump(Gnew.mapDummyToRealDic, f)
with open(folderName + "xResolvedSimplifiedList.json", "w") as f:
json.dump(Gnew.xResolvedSimplifiedList, f)
def BResolution(Gnew, folderName, contigReadGraph, N1, myCountDic, lenDic):
if abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve:
print "abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve", abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve
maxRThres = abunHouseKeeper.abunGlobalSplitParameterRobot.RThres
repeatFinder.adjListToRepeatList(Gnew.adj, folderName, "phaseRepeatTR.txt")
json_data = open(folderName + "phaseRepeatTR.txt", "r")
repeatPairs = json.load(json_data)
repeatPairs = obtainNonEmpty(repeatPairs)
biResolvedCombineList = []
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
Grev = abunGraphLib.formReverseGraphFast(G)
abunAnalysisList = []
for eachitem in repeatPairs:
inList, outList = eachitem[0], eachitem[1]
resolvedList, brResolvedList = [], []
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunAbunB:
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerB > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLower = (
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerB
)
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperB > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpper = (
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperB
)
if not abunHouseKeeper.abunGlobalSplitParameterRobot.toRunAggB:
resolvedList = determindMatch(inList, outList, myCountDic, folderName, contigReadGraph, N1)
else:
resolvedList = determindMatchAggregate(
inList, outList, myCountDic, folderName, contigReadGraph, N1, Gnew, lenDic
)
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunBRB:
if abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresB > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThres = (
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresB
)
brResolvedList = formBRReolve(folderName, inList, outList, G, Grev, True, N1)
combinedList = abunHouseKeeper.getDistinct(resolvedList + brResolvedList)
print "resolvedList, brResolvedList, inList, outList", resolvedList, brResolvedList, inList, outList
print "resolveConflict(combinedList)", resolveConflict(combinedList)
abunAnalysisList.append([inList, outList, resolvedList, brResolvedList, resolveConflict(combinedList)])
if len(inList) <= maxRThres and len(outList) <= maxRThres and len(inList) > 0 and len(outList) > 0:
# biResolvedCombineList += resolveConflict(combinedList)
resolvedCombine = resolveConflict(combinedList)
### kkdebug
Gnew.bipartiteLocalResolve(resolvedCombine, inList, outList, folderName)
# json_data = open(folderName + "hackBRResolveList.json", 'r')
# dataItem = json.load(json_data)
# Gnew.bipartiteResolve(dataItem)
### end kkdebug
Gnew.condense()
with open(folderName + "biResolvedCombineList.json", "w") as f:
json.dump(biResolvedCombineList, f)
with open(folderName + "abunAnalysisList.json", "w") as f:
json.dump(abunAnalysisList, f)
# assert(1==2)
return Gnew
else:
return Gnew
def BResolution(Gnew, folderName, contigReadGraph, N1, myCountDic, lenDic,
mummerLink):
if abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve:
print "abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve", abunHouseKeeper.abunGlobalSplitParameterRobot.runBResolve
maxRThres = abunHouseKeeper.abunGlobalSplitParameterRobot.RThres
repeatFinder.adjListToRepeatList(Gnew.adj, folderName,
"phaseRepeatTR.txt")
json_data = open(folderName + "phaseRepeatTR.txt", 'r')
repeatPairs = json.load(json_data)
repeatPairs = obtainNonEmpty(repeatPairs)
biResolvedCombineList = []
G = abunGraphLib.seqGraphWt(0)
G.loadFromFile(folderName, contigReadGraph)
Grev = abunGraphLib.formReverseGraphFast(G)
abunAnalysisList = []
for eachitem in repeatPairs:
inList, outList = eachitem[0], eachitem[1]
if not abunHouseKeeper.abunGlobalRunEM:
resolvedList, brResolvedList = [], []
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunAbunB:
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerB > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLower = abunHouseKeeper.abunGlobalSplitParameterRobot.AbunLowerB
if abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperB > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpper = abunHouseKeeper.abunGlobalSplitParameterRobot.AbunUpperB
if not abunHouseKeeper.abunGlobalSplitParameterRobot.toRunAggB:
resolvedList = determindMatch(inList, outList,
myCountDic, folderName,
contigReadGraph, N1)
else:
resolvedList = determindMatchAggregate(
inList, outList, myCountDic, folderName,
contigReadGraph, N1, Gnew, lenDic)
if abunHouseKeeper.abunGlobalSplitParameterRobot.toRunBRB:
if abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresB > 0:
abunHouseKeeper.abunGlobalSplitParameterRobot.BRThres = abunHouseKeeper.abunGlobalSplitParameterRobot.BRThresB
brResolvedList = formBRReolve(folderName, inList, outList,
G, Grev, True, N1)
combinedList = abunHouseKeeper.getDistinct(resolvedList +
brResolvedList)
print "resolvedList, brResolvedList, inList, outList", resolvedList, brResolvedList, inList, outList
print "resolveConflict(combinedList)", resolveConflict(
combinedList)
abunAnalysisList.append([
inList, outList, resolvedList, brResolvedList,
resolveConflict(combinedList)
])
if len(inList) <= maxRThres and len(
outList) <= maxRThres and len(inList) > 0 and len(
outList) > 0:
resolvedCombine = resolveConflict(combinedList)
Gnew.bipartiteLocalResolve(resolvedCombine, inList,
outList, folderName)
else:
import emalgo
resolvedCombine = emalgo.BResolvePreparation(
folderName, inList, outList, G, Grev, N1, mummerLink)
Gnew.bipartiteLocalResolve(resolvedCombine, inList, outList,
folderName)
Gnew.condense()
with open(folderName + "biResolvedCombineList.json", 'w') as f:
json.dump(biResolvedCombineList, f)
with open(folderName + "abunAnalysisList.json", 'w') as f:
json.dump(abunAnalysisList, f)
#assert(1==2)
return Gnew
else:
return Gnew
