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NameError                                 Traceback (most recent call last)
<ipython-input-12-b6e7823afcf5> in <module>()
     17 
     18 print(outputPath, pickleDir)
---> 19 main(data_directory, tag, outputPath, manualThresholdNumber)

<ipython-input-12-b6e7823afcf5> in main(data_directory, tag, outputPath, manualThresholdNumber)
      4     date_time = datetime.datetime.now()
      5     print(date_time.strftime("%Y-%b-%d %H:%M"))
----> 6     startClustering(data_directory, tag, outputPath, manualThresholdNumber)
      7     date_time = datetime.datetime.now()
      8     print(date_time.strftime("%Y-%b-%d %H:%M"))

<ipython-input-11-1e4aa6d47375> in startClustering(data_directory, tag, outputPath, thresholdValue)
     17                                                                                tag,
     18                                                                                outputPath,
---> 19                                                                                thresholdValue)
     20 
     21     # saving intermediatePool as pickle file

<ipython-input-11-bac1e31319dc> in do_RasMMA_clustering(data_directory, tag, outputPath, thresholdValue)
     37 
     38         # calculate scoreList in candidate clusters
---> 39         scoreList = findMergeCandidateScoreList(toMergeCandidateDict, generatedSeqNum)
     40         # check and merge exactly the same candidates before merge clusters
     41         scoreList = checkExactlySameCandidates(scoreList)

<ipython-input-11-36e0a55e1990> in findMergeCandidateScoreList(toMergeCandidateDict, generatedSeqNum)
     12             Ri = toMergeCandidateDict[ dictKeys[i] ][0]
     13             Rj = toMergeCandidateDict[ dictKeys[j] ][0]
---> 14             repNew_CMS = get_Rep_CommMotifSeq(Ri, Rj) # get rep's common motif seq.
     15             clusterTempName = "G" + str(generatedSeqNum)
     16             Rnew = (clusterTempName, repNew_CMS)

<ipython-input-11-4c0f20e12e7a> in get_Rep_CommMotifSeq(Ri, Rj)
     13         commonSequence = do_globalAlignment(rep1, rep2) # do Alignment
     14         repNew = commonSequence
---> 15     return repNew

NameError: name 'repNew' is not defined

def get_Rep_CommMotifSeq(Ri, Rj):
    global repNew
    rep1 = []
    for motif in Ri[1]:
        rep1.extend(motif)
    rep2 = []
    for motif in Rj[1]:
        rep2.extend(motif)
    repNew_CMS = []
    if(rep1 and rep2):
        commonSequence = do_globalAlignment(rep1, rep2) # do Alignment
        repNew = commonSequence
    return repNew

ZeroDivisionError                         Traceback (most recent call last)
<ipython-input-21-f51fb98ae00c> in <module>()
     17 
     18 print(outputPath, pickleDir)
---> 19 main(data_directory, tag, outputPath, manualThresholdNumber)

<ipython-input-21-f51fb98ae00c> in main(data_directory, tag, outputPath, manualThresholdNumber)
      4     date_time = datetime.datetime.now()
      5     print(date_time.strftime("%Y-%b-%d %H:%M"))
----> 6     startClustering(data_directory, tag, outputPath, manualThresholdNumber)
      7     date_time = datetime.datetime.now()
      8     print(date_time.strftime("%Y-%b-%d %H:%M"))

<ipython-input-11-1e4aa6d47375> in startClustering(data_directory, tag, outputPath, thresholdValue)
     17                                                                                tag,
     18                                                                                outputPath,
---> 19                                                                                thresholdValue)
     20 
     21     # saving intermediatePool as pickle file

<ipython-input-11-bac1e31319dc> in do_RasMMA_clustering(data_directory, tag, outputPath, thresholdValue)
     37 
     38         # calculate scoreList in candidate clusters
---> 39         scoreList = findMergeCandidateScoreList(toMergeCandidateDict, generatedSeqNum)
     40         # check and merge exactly the same candidates before merge clusters
     41         scoreList = checkExactlySameCandidates(scoreList)

<ipython-input-11-36e0a55e1990> in findMergeCandidateScoreList(toMergeCandidateDict, generatedSeqNum)
     15             clusterTempName = "G" + str(generatedSeqNum)
     16             Rnew = (clusterTempName, repNew_CMS)
---> 17             score = compute_Score(Ri, Rj, Rnew)
     18             Ri_name = Ri[0]
     19             Rj_name = Rj[0]

<ipython-input-11-896931b6b6bc> in compute_Score(Ri, Rj, Rnew)
     18         Lorg = max(L_Ri, L_Rj)
     19         Lnew = len(repNew)
---> 20         return float(Lnew)/Lorg
     21     else:
     22         return 0

ZeroDivisionError: float division by zero

# compute score of Rnew
# the score calculate method is the length ratio of new to origin one

# Ri is a tuple like ('G0', [['A#A', 'C#C'],['D#D']])
def compute_Score(Ri, Rj, Rnew):
    if(Rnew[1]):
        repI = []
        for API_motif in Ri[1]:
            repI.extend(API_motif)
        repJ = []
        for API_motif in Rj[1]:
            repJ.extend(API_motif)
        repNew = []
        for API_motif in Rnew[1]:
            repNew.extend(API_motif)
        L_Ri = len(repI)
        L_Rj = len(repJ)
        Lorg = max(L_Ri, L_Rj)
        Lnew = len(repNew)
        return float(Lnew)/Lorg
    else:
        return 0