5.py

with open('E_coli.txt', 'r') as file:
    E_coli_Genome = file.read().rstrip()

def FrequencyTable(Text, k):
    freqMap  = {}
    n  = len(Text)
    # print(f"n = {n}")
    for i in range(n-k):
        Pattern = Text[i:i+k] #← Text(i, k)
        # print(f"Pattern: {Pattern}")
        if Pattern not in freqMap: #freqMap[Pattern] doesn't exist
            freqMap[Pattern] = 1
        else:
           freqMap[Pattern] = freqMap[Pattern]+1 
    return freqMap


def BetterFrequentWords(Text, k):
    FrequentPatterns = [] 
    freqMap = FrequencyTable(Text, k)
    # max ← MaxMap(freqMap)
    maxVal = max(freqMap.values())
    for Pattern in freqMap:
        if freqMap[Pattern] == maxVal:
            FrequentPatterns.append(Pattern)
    return FrequentPatterns

def FindClumps(Text, k, L, t):
    Patterns = [] # an array of strings of length 0
    n = len(Text)
    ran = n-L
    for i in range(ran):
        Window = Text[i: i+L]
        freqMap = FrequencyTable(Window, k)
        for s in freqMap.keys():
            if freqMap[s] >= t:
                Patterns.append(s)
    # remove duplicates from Patterns
    Patterns = list(set(Patterns))
    return Patterns

# print(FindClumps('CGGACTCGACAGATGTGAAGAACGACAATGTGAAGACTCGACACGACAGAGTGAAGAGAAGAGGAAACATTGTAA', 5, 50, 4))

# sample = 'AACCCTGTACGTTCGCTGACTTACGTCCGCTTTGTAGGTGATTGGTACTCCTCAGGCATCACGGCCGGTCGATGAGGTAGATCGAAGCCCATGCAGAACTGGCCATTATCGTCACCAAGTGCGTAGTGCAAGAAACACTGCCGGCCTACCAACACAAAATGTTTCTACCGGAGACCTGGTATGTGGAGGAATTCTTTTGCCAAACACCGAGCAATACCGGAAGACTGCAGTACTTTAACGTGTTTAATGAGTACGATATCCTTGCGGCAGGGACACCCTCCCCTCTAACCAAGAGCGTAGGGACCGCCTGAACTTACAATTAGTGTGCAAGCGGTCAATTGCCTTGGCCCAGCATTGTTAAAGGCTCTGACGGCAAACTCGTCACTAGGCGAAAGCTAGAGTAATTCTAGCAGGAATGATGGGAATGTGTCGCACATCTAGATCGCAGGGTACTTATGTTGGACATTATTAGGAAGTGTCAGAGCTCCTGGCTACGACCTGGCTACTGGCTACGACGGGTCTCCTGGGCAGACAAGTAGGGGACCCAATCACAAGTGTAGTGGAAAAACGTGGTCGAGGACAGTATCTATCGCCAACGAATCTCGGTCAAGTTGGGCTGCGCACATCAGCTATGTTACTATAGGCAAGGATGGTGACCGGGTTTATAGCTATTTTAAAGCAATGTAGAGCCTAACGCCTGAGCGGGCCCTGGAAAAAAGAAAACATACACTTCTCCCTAAATGGCACGTGGACGCGACAAATGACATACCTTCATATTCTTTAAGCTGAGATCTTTTTTAAGCTGATGAGTGTTGTCCGTTGAGGTGAGTACAGGCTGGGACGGGACGACGCTGGGACCAAACATTACATTGTAGTCGTTTAAGTTTTTAAGTTTAGGGAAACACGAGTGCCCGACTAAAGATCCGCATCGATGGTGCACATATTGCAACGCTCCCTTCGTGTACAATTGTACAATGGAATGGCAATGGCGCGTCCCTCGCGACGTATTGAAGGCTATACAGTCACTCCACTCCTAATCTCCACTCCTAATTTGCAGCTCTCGTAGAATCAAGTCTTCCCTTCCGTAAGCTCTCTAACCATTGAGATTCCGAAATTGAGATTCGTGCACAGGTTCGTCCGTCGATTGTACGCACGCAGGGTACGGGTACTACGGTTAACTTGCAACGCCTTCTTGAGTCTACTGTGGGTATTGACGCCGTGTAATGATTTATAGACGCTAAAGTCGCCTCTGGTCATACTAGGACGAAATATTCTAGCCGCGCACCAATAGCAGCTAAGAAACCACTTAAGCAACTTAGCGATGGGTTTCACAGCGGGTTGGCTAACGATGGCTTACAAAGAATTTTTGTTCTCTTTTGTTGACGACTTTATGGGTATGGGACTTTATGGTGATTGCTCTGACTACTGCTGACCTGACTATGGGGGCCTGATTGACCCATGCATTCCCTGTCCATCCACTCCGGTGGTGAAGGAGCGGCTACACACCTGTACAATTAATATCGAGCGATTTATTTATAGCGATTTATTATCGGCGCAGCGGTCTCCTGATGAAGACAGGGGACAGGAAGACAGGGCCCTCGAACTCGAAAGATTTTTACCAGAGTTTAGAACGCGGATAAGGGCAAGAAAGGATTGTAATGTCCATTTGTCCTCTCCGTAATCGCCCCAACCGCGAATGACGGGAGCCAACGGAACGGGAGCCACACACCACAAAACGTCATTCTCCCCACTATGTAATACGTTAGCACCCCCCCTATTGCATGTCTCCTAAAGGTGTAACCAAGAGGACTGCTTTTGACTGCTTTTGACTGCTTTTGACTGCTTTTAGACTGCTTTTAGTTAACGGGAGTTAACGGGAGTTAACGGGAGTTAACGGGATGTCGCTGTCGCAGTGTGTCGCAGTGGTGAGTTAACGGG'
# print(FindClumps(sample, 10, 25, 4))

print(FindClumps(E_coli_Genome, 9, 500, 3))