def branchClearingUnitTest(G, N, L,K, liid, threshold, foldername = "",branchingDepth= 20): dummyParameters = logging.parameterObj() dummyParameters.defaultFolder = foldername dummyParameters.brachingDepth = branchingDepth dummyParameters.K, dummyParameters.liid, dummyParameters.threshold = K, liid, threshold dummyParameters.G, dummyParameters.N, dummyParameters.L = G, N, L motherGen, reads, noisyReads = logging.rawDataLoad(foldername+"UnitTest",G,N,L, "dn") returnfmapping= logging.fmappingLoad(foldername+'clusteredGroup.csv') G1,startList, fmapping = graphForm.getSeqGraph(returnfmapping,noisyReads, dummyParameters) #checkCondensingBasic(G1, startList, "simple") returnfmapping, G1= branchClear.clearResidual(returnfmapping,G1,dummyParameters) G2 = G1 graphForm.debugSeqGraph(G2) #G2 = G1 checkCondensingBasic2(G2, [G2[0]], "simple")
def runAssembler(snpRate, typeOfGen, detail, parameterRobot): #N, G, L, p,K,snpRate, typeOfGen, detail = 100, 100, 10000, 0.01,30,0.001, 'r', "1000" motherGen, reads, noisyReads = dataGen.generateData( typeOfGen, detail, parameterRobot) motherGen, reads, noisyReads = logging.rawDataLoad( parameterRobot.defaultFolder + "UnitTest", parameterRobot.G, parameterRobot.N, parameterRobot.L, "dn") f1 = cluster.groupIndelNoisyKmers(noisyReads, parameterRobot) G1, startList, f1 = graphForm.getSeqGraph(f1, noisyReads, parameterRobot) f2, G2 = branchClear.clearResidual(f1, G1, parameterRobot) G3 = bridgeResolve.resolveRepeats(f2, G2, parameterRobot) G4 = alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate, parameterRobot) #G4 = G3 recovSeq = eulerCycle.findEC(G4) recovGen = readAns.reportRecovSeq(recovSeq, f2, noisyReads, parameterRobot) numMistakes, success = compare.subAlignCompare(recovGen, motherGen, parameterRobot) #numMistakes, success = 0 , 0 return numMistakes, success # Target of the new code : Fast Assemble and assembly in optimal amount of information #t0 = time.time() #N, G, L, p,snpRate, typeOfGen, detail = 1000, 10000,200, 0.015, 0.001 ,'m', "500-300-50" #runAssembler(N, G, L, p,snpRate, typeOfGen, detail) #print "Time (sec) :", time.time() - t0
def branchClearingUnitTest(G, N, L, K, liid, threshold, foldername="", branchingDepth=20): dummyParameters = logging.parameterObj() dummyParameters.defaultFolder = foldername dummyParameters.brachingDepth = branchingDepth dummyParameters.K, dummyParameters.liid, dummyParameters.threshold = K, liid, threshold dummyParameters.G, dummyParameters.N, dummyParameters.L = G, N, L motherGen, reads, noisyReads = logging.rawDataLoad(foldername + "UnitTest", G, N, L, "dn") returnfmapping = logging.fmappingLoad(foldername + 'clusteredGroup.csv') G1, startList, fmapping = graphForm.getSeqGraph(returnfmapping, noisyReads, dummyParameters) #checkCondensingBasic(G1, startList, "simple") returnfmapping, G1 = branchClear.clearResidual(returnfmapping, G1, dummyParameters) G2 = G1 graphForm.debugSeqGraph(G2) #G2 = G1 checkCondensingBasic2(G2, [G2[0]], "simple")
def runAssembler(snpRate, typeOfGen, detail,parameterRobot): #N, G, L, p,K,snpRate, typeOfGen, detail = 100, 100, 10000, 0.01,30,0.001, 'r', "1000" motherGen, reads, noisyReads = dataGen.generateData(typeOfGen, detail,parameterRobot) motherGen, reads, noisyReads = logging.rawDataLoad(parameterRobot.defaultFolder+"UnitTest",parameterRobot.G,parameterRobot.N,parameterRobot.L, "dn") f1 = cluster.groupIndelNoisyKmers(noisyReads,parameterRobot) G1,startList, f1 = graphForm.getSeqGraph(f1,noisyReads, parameterRobot) f2, G2 = branchClear.clearResidual(f1, G1,parameterRobot) G3 = bridgeResolve.resolveRepeats(f2, G2,parameterRobot) G4 = alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate,parameterRobot ) #G4 = G3 recovSeq = eulerCycle.findEC(G4) recovGen = readAns.reportRecovSeq(recovSeq, f2, noisyReads,parameterRobot) numMistakes, success = compare.subAlignCompare(recovGen, motherGen,parameterRobot) #numMistakes, success = 0 , 0 return numMistakes, success # Target of the new code : Fast Assemble and assembly in optimal amount of information #t0 = time.time() #N, G, L, p,snpRate, typeOfGen, detail = 1000, 10000,200, 0.015, 0.001 ,'m', "500-300-50" #runAssembler(N, G, L, p,snpRate, typeOfGen, detail) #print "Time (sec) :", time.time() - t0