temp = [] something = [] # j is the fragment count +=1 # print j #Bases Frequencies #findBasesFrequency(j) = Afrequency, Tfrequency, Gfrequency, Cfrequency temp = findBasesFrequency(j) #line = np.hstack((line, temp)) # print "temp", temp # print "temp size", len(temp) # print "" dimers,trimers,dimercounts,trimercounts = find_kmers(j) # print "dimers",dimers # print "j",j # print "dimercounts",dimercounts # exit() maxNoDimers = float(windowSize-1) # The length of each window is 10 maxNoTrimers = float(windowSize-2) for dim in dimercounts: if maxNoDimers != 0: something.append(dim/maxNoDimers) else: something.append(dim) for trim in trimercounts:
exit()
y1 = sumEsetSequences
y1 ='{0:.10f}'.format(y1)
print y1
exit()
y2 = actualArrayWithNames[:,-1]
x = np.arange(len(y1))
plotTwoScales(x, 'samples', y1, 'Summations', y2, 'InitRates', 'SummedValues from CE', 'Initiation Rates (log)', 'Gritsenko/plotSummations.png')
exit()
########
# Conditional Entropy per 3-mer
dimers,trimers,dimercounts,trimercounts = find_kmers('ATGC')
trimers = np.array(trimers) # 64 possibilities
essetTrimers = []
for k in range(maxLength-3):
tempSequences = []
#Select the sequences that have this length
for s in range(len(sortedArray)):