Exemplo n.º 1
0
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 
Exemplo n.º 3
0
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 
Exemplo n.º 4
0
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