def betterClumpFinding(Genome, k, t, L):
genomeList = list(Genome)
frequentPatterns = []
clump = []
for i in range(4**k - 1 + 1):
clump.insert(i, 0)
text = Genome[0:L]
frequencyArray = computingFreqs(text, k)
for i in range(4**k - 1 + 1):
if frequencyArray[i] >= t:
clump[i] = 1
for i in range(len(genomeList) - L + 1):
firstPattern = Genome[i - 1:i - 1 + k]
index = patternToNumber(firstPattern)
frequencyArray[index] = frequencyArray[index] - 1
lastPattern = Genome[i + L - k:i + L - k + k]
index = patternToNumber(lastPattern)
frequencyArray[index] = frequencyArray[index] + 1
if frequencyArray[index] >= t:
clump[index] = 1
for i in range(4**k):
if clump[i] == 1:
pattern = numberToPattern(i, k)
frequentPatterns.append(pattern)
return frequentPatterns
def betterClumpFinding(Genome, k, t, L):
genomeList = list(Genome)
frequentPatterns = []
clump = []
for i in range(4**k - 1 + 1):
clump.insert(i, 0)
text = Genome[0:L]
frequencyArray = computingFreqs(text,k)
for i in range(4**k-1+1):
if frequencyArray[i] >= t:
clump[i] = 1
for i in range(len(genomeList) - L + 1):
firstPattern = Genome[i-1:i-1+k]
index = patternToNumber(firstPattern)
frequencyArray[index] = frequencyArray[index]-1
lastPattern = Genome[i+L-k:i+L-k+k]
index = patternToNumber(lastPattern)
frequencyArray[index] = frequencyArray[index]+1
if frequencyArray[index] >= t:
clump[index] = 1
for i in range(4**k):
if clump[i] == 1:
pattern = numberToPattern(i,k)
frequentPatterns.append(pattern)
return frequentPatterns
def computingFreqs(Text, k):
frequencyArray = []
for i in range(4**k - 1 + 1):
frequencyArray.insert(i, 0)
for i in range(len(Text) - k + 1):
pattern = Text[i:i + k]
j = patternToNumber(pattern)
frequencyArray[j] += 1
return frequencyArray
def computingFreqs(Text, k):
textList = list(Text)
frequencyArray = []
for i in range(4**k-1+1):
frequencyArray.insert(i, 0)
for i in range(len(textList)-k+1):
pattern = textList[i:i+k]
j = patternToNumber(pattern)
x = frequencyArray[j] + 1
frequencyArray[j] += 1
return frequencyArray