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):
frequentPatterns = []
frequencyArray = computingFreqs(Text,k)
maxCount = max(frequencyArray)
for i in range(4**k-1+1):
if frequencyArray[i] == maxCount:
pattern = numberToPattern(i,k)
frequentPatterns.append(pattern)
return frequentPatterns
def computingFreqs(Text, k):
frequentPatterns = []
frequencyArray = computingFreqs(Text, k)
maxCount = max(frequencyArray)
for i in range(4**k - 1 + 1):
if frequencyArray[i] == maxCount:
pattern = numberToPattern(i, k)
frequentPatterns.append(pattern)
return frequentPatterns
def clumpFinding(Genome, k, t, L):
genomeList = list(Genome)
frequentPatterns = []
clump = []
for i in range(4**k - 1 + 1):
clump[i] = 0
for i in range(len(genomeList) - L + 1):
text = genomeList[i:i + L]
frequencyArray = computingFreqs(text, k)
for index in range(4**k - 1 + 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 clumpFinding(Genome, k, t, L):
genomeList = list(Genome)
frequentPatterns = []
clump = []
for i in range(4**k - 1 + 1):
clump[i] = 0
for i in range(len(genomeList) - L + 1):
text = genomeList[i:i+L]
frequencyArray = computingFreqs(text,k)
for index in range(4**k-1+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
from numberToPattern import numberToPattern
from computingFrequencies import computingFreqs
def computingFreqs(Text, k):
frequentPatterns = []
frequencyArray = computingFreqs(Text,k)
maxCount = max(frequencyArray)
for i in range(4**k-1+1):
if frequencyArray[i] == maxCount:
pattern = numberToPattern(i,k)
frequentPatterns.append(pattern)
return frequentPatterns
if __name__ == "__main__":
Text = "ACGTTGCATGTCGCATGATGCATGAGAGCT"
k = 4
result = computingFreqs(Text, k)
print result
from numberToPattern import numberToPattern
from computingFrequencies import computingFreqs
def computingFreqs(Text, k):
frequentPatterns = []
frequencyArray = computingFreqs(Text, k)
maxCount = max(frequencyArray)
for i in range(4**k - 1 + 1):
if frequencyArray[i] == maxCount:
pattern = numberToPattern(i, k)
frequentPatterns.append(pattern)
return frequentPatterns
if __name__ == "__main__":
Text = "ACGTTGCATGTCGCATGATGCATGAGAGCT"
k = 4
result = computingFreqs(Text, k)
print result
