def batchProcessingUnitTest(numberOfRounds, parameterRobot, snpRate, typeOfGen, detail): print "Batch Processing Unit Test : " #snpRate, typeOfGen, detail = 0.001 ,'d', "genome.fasta-10000-20000" resultList = [] oldName = parameterRobot.defaultFolder for index in range(numberOfRounds): tempfile = open(oldName + "/result.txt", 'a') os.system("mkdir " + oldName + "/round_" + str(index)) parameterRobot.defaultFolder = oldName + "/round_" + str(index) + "/" #try: numMistakes, success = assemblerMain.runAssembler( snpRate, typeOfGen, detail, parameterRobot) # except: # numMistakes, success= parameterRobot.G, False print[numMistakes, success] resultList.append([numMistakes, success]) print "index, resultList", index, resultList tempfile.write( str(parameterRobot.N) + " " + str(parameterRobot.L) + " " + str(index) + " " + str(numMistakes) + ", " + str(success) + "\n") tempfile.close() # Print result print "results( N, L )", parameterRobot.N, parameterRobot.L for eachitem in resultList: print "eachitem", eachitem
def batchProcessingUnitTest(numberOfRounds,parameterRobot,snpRate, typeOfGen , detail): print "Batch Processing Unit Test : " #snpRate, typeOfGen, detail = 0.001 ,'d', "genome.fasta-10000-20000" resultList = [] oldName = parameterRobot.defaultFolder for index in range(numberOfRounds): tempfile = open(oldName+"/result.txt", 'a') os.system("mkdir "+ oldName + "/round_" +str(index) ) parameterRobot.defaultFolder = oldName + "/round_" +str(index) + "/" #try: numMistakes, success = assemblerMain.runAssembler(snpRate, typeOfGen, detail,parameterRobot) # except: # numMistakes, success= parameterRobot.G, False print [numMistakes, success] resultList.append([numMistakes, success]) print "index, resultList",index, resultList tempfile.write(str(parameterRobot.N) +" " + str(parameterRobot.L) +" " + str(index) +" " + str(numMistakes) + ", " + str(success) + "\n") tempfile.close() # Print result print "results( N, L )",parameterRobot.N, parameterRobot.L for eachitem in resultList: print "eachitem", eachitem
def overallTestRun(): #"oneLine.fasta-0-1440371" G, N, L, p, epsilon, K, liid, threshold,NKcov, Nbridge, Ncov, ratio, numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth,folderName =10000 ,83 , 1189, 0.01 , 0.1 , 600 , 32, 8 , 508 , 377 , 417 , 1.21822542 , 0, 0, 0 , 0 , "" parameterRobot = logging.parameterObj(G, N, L, p, epsilon, K, liid, threshold,NKcov, Nbridge, Ncov, ratio, numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth,folderName ) snpRate, typeOfGen, detail = 0.001 ,'d', "genome.fasta-50000-60000" parameterRobot.clusterRounds , parameterRobot.fingerPrint, parameterRobot.clusterRatio = 2 , 6, 1 #snpRate, typeOfGen , detail = 0.001,'m', "500-200-50" numMistakes, success = assemblerMain.runAssembler(snpRate, typeOfGen, detail, parameterRobot) return numMistakes, success
def overallTestRun(): #"oneLine.fasta-0-1440371" G, N, L, p, epsilon, K, liid, threshold, NKcov, Nbridge, Ncov, ratio, numberOfClusterRounds, brachingDepth, bridgingDepth, msaWidth, folderName = 10000, 83, 1189, 0.01, 0.1, 600, 32, 8, 508, 377, 417, 1.21822542, 0, 0, 0, 0, "" parameterRobot = logging.parameterObj(G, N, L, p, epsilon, K, liid, threshold, NKcov, Nbridge, Ncov, ratio, numberOfClusterRounds, brachingDepth, bridgingDepth, msaWidth, folderName) snpRate, typeOfGen, detail = 0.001, 'd', "genome.fasta-50000-60000" parameterRobot.clusterRounds, parameterRobot.fingerPrint, parameterRobot.clusterRatio = 2, 6, 1 #snpRate, typeOfGen , detail = 0.001,'m', "500-200-50" numMistakes, success = assemblerMain.runAssembler(snpRate, typeOfGen, detail, parameterRobot) return numMistakes, success