def betterclumpfinding(genome, k, t, L):
frequentpatterns = []
clump = []
for i in range(0, pow(4, k)):
clump.append(0)
text = genome[0:L]
freqArray = computingfrequencies.computing_frequencies(text, k)
for i in range(0, pow(4, k)):
if freqArray[i] >= t:
clump[i] = 1
for i in range(1, len(genome) - L + 1):
firstPattern = genome[i - 1 : i - 1 + k]
index = computingfrequencies.patternToNumber(firstPattern)
freqArray[index] = freqArray[index] - 1
lastPattern = genome[i + L - k : i + L]
index = computingfrequencies.patternToNumber(lastPattern)
freqArray[index] = freqArray[index] + 1
if freqArray[index] >= t:
clump[index] = 1
for i in range(0, pow(4, k)):
if clump[i] == 1:
pattern = numberToPattern(i, k)
frequentpatterns.append(pattern)
return frequentpatterns
def betterclumpfinding(genome, k, t, L):
frequentpatterns = []
clump = []
for i in range(0, pow(4, k)):
clump.append(0)
text = genome[0:L]
freqArray = computingfrequencies.computing_frequencies(text, k)
for i in range(0, pow(4, k)):
if freqArray[i] >= t:
clump[i] = 1
for i in range(1, len(genome) - L + 1):
firstPattern = genome[i - 1:i - 1 + k]
index = computingfrequencies.patternToNumber(firstPattern)
freqArray[index] = freqArray[index] - 1
lastPattern = genome[i + L - k:i + L]
index = computingfrequencies.patternToNumber(lastPattern)
freqArray[index] = freqArray[index] + 1
if freqArray[index] >= t:
clump[index] = 1
for i in range(0, pow(4, k)):
if clump[i] == 1:
pattern = numberToPattern(i, k)
frequentpatterns.append(pattern)
return frequentpatterns
def clumpfinding(genome, k, t, L):
frequentpatterns = []
clump = []
for i in range(0, pow(4, k)):
clump.append(0)
for i in range(0, len(genome) - L + 1):
text = genome[i : i + L]
freqArray = computingfrequencies.computing_frequencies(text, k)
for indx in range(0, pow(4, k)):
if freqArray[indx] >= t:
clump[indx] = 1
for i in range(0, pow(4, k)):
if clump[i] == 1:
pattern = numberToPattern(i, k)
frequentpatterns.append(pattern)
return frequentpatterns
def clumpfinding(genome, k, t, L):
frequentpatterns = []
clump = []
for i in range(0, pow(4, k)):
clump.append(0)
for i in range(0, len(genome) - L + 1):
text = genome[i:i + L]
freqArray = computingfrequencies.computing_frequencies(text, k)
for indx in range(0, pow(4, k)):
if freqArray[indx] >= t:
clump[indx] = 1
for i in range(0, pow(4, k)):
if clump[i] == 1:
pattern = numberToPattern(i, k)
frequentpatterns.append(pattern)
return frequentpatterns
