clump_finder.py

import textwrap


def ClumpFinding(dna, length_of_k_mer, length_of_chunk_to_search_in, total_number_of_occurrence):
    motifs = {}
    most_repeated_motifs = {}
    chunks_of_dna = []
    number_of_chunk = 1
    for chunk in textwrap.wrap(dna, length_of_chunk_to_search_in):
        chunks_of_dna.append(chunk)

    for chunk in chunks_of_dna:
        for i in range(0, len(chunk)):
            motif_frq = chunk[i:i + length_of_k_mer]
            if len(motif_frq) == length_of_k_mer:
                if motif_frq in motifs:
                    motifs[motif_frq] += 1

                else:
                    motifs[motif_frq] = 1

    for key, val in motifs.items():
        if motifs[key] >= total_number_of_occurrence:
            most_repeated_motifs[key] = val
    number_of_chunk += 1

    return f'{[x for x in most_repeated_motifs]} is\\are the most repeated {length_of_k_mer}-mer in chunk of length {length_of_chunk_to_search_in}'


dna = 'TACCGAACGTACATTGACTGCGACGCTAGGTTGGATAGTAGGCTGCTAACAGGCGCAGTGTGGCGCACGAGTCTTACACTACATGTATGCTTAAGATAGTGTATGAGACTCCAGGCCACTATGGGTGCAGCGAAACCTCGAGAGATCAGATCAGATCCTGGATAGATGACACGTAATCCAACTTCCTGATATATTGTAAATTGTAACTTACTTTACGAAACCTAGGGTGAGGGTGATTAGGGTGATGACCTTTAGATCTTTCCTAGCCTGGCCAACGCCCGAGGTACACATGGTGGTTCCGTTAAACCATGGATTCTCAACCTGGAACCGGCTCATTGGCATTCTTCACTGCAAGAACGGAAGTGCCCGCCTTGAGACGAAGCGTCACTCGTCGGGTTTTGCGTATGTATTGTTGTTGCGTATTGACGCCGCGGATTACCGTCCTCCCTATATGTTCTCGGGGGACGAAACGCGACCACGCGCAGGGCAACGCGGCAAACCGGGGTACACCGCGGAATTATCTAGTCTAGGGGGACCGGGACCAGCCGGGACCAGGTTTTACTCTCCGTGCCGCGACAGATAGTTAGCCAAAGGCGCACATGGTGCTAGGACCCTCTGTGAGGCTCCGCGCATTCAGGGCGGTCGGGCGTGATACAGTGGATTTGAGTTGTAGTCGACACCTAGGGTGTTCAATTGAACAGGTGACTCTCCACAGTTCCCATCGAGCCTTGGGGTAAAACGCAGGTCTTATAAAACTTGTGCTGTATAGTTAGGGAATGTAACACGTGTCTTAGCTCAGAGAGCCCTAGTCCCATCGGTTGGGGAATATACTATCCACGCGTAGCCTAAAGACCCCGCCGGGAATTATAAAATTCTCTTGTCACCACAGATTGCTGGAGGGCGGACTCTGATACCCCAGACCGGGACTACGGACTACCACCCCACCAGACAACTAACGACATACCTGTTAGAGTGGTGCTCTATGTGGGGAACAGTAGATCCATTCCATCAAACATACTGTCTTGTAGCTTACATTTGCTCTCCTATGAAAGCACGCATGAGAGTAGATTCTTGTTTCGCTTTGCCGTCTTGCTTCTTGCTTTGCTCTTGCTTATGCGGTGTGTGTAAAAAAAAGTGTAAAACTGGCGTATCGCTTACTTTAAACACTTACCGCTGTTTGACCGCAGGCCTGTGCGGTCCGTACTTGCACAAAAGTGGCACTGTTAGGCACTCCTTTAGCTCTGATAGTAGGTGAACCCGGGGTCACTTGAAAGAACTGTACTAACCATCCTCTCGAGGCGGGTTCGGTTGCCATGCTGCAGCATGTTATCCTCTCCGTAATCTCTCCGTAAAAAAGCGGTAAAGCGGTTTACTCGGACCAGGTGCACTTCCAGCGTCTCCCTAGTCTAATTTTACGCTGATCACTACACAGATACACCGCCGGCACTGACTGTTGCATACCCTCGGTTGCCGAATTGCCTATCGCAACAACACCACCCCTACAACACCTCGGAGCATCTCCGTGCAGCGTTAGGCTGCTTCATATTGACTACTAGCCACTGTTAGACCATCTGCTGTGAGACACACACGTACACGGATCTACCTTGGGGTAGTTGGAAAGGGATTGGATTGGTACCGCGTGCTTCGGTCGTGCTTCCTGCTTCTCCCGATTGGCCGTAACACAGGCAGAACCCCCGTTGGCGTGACCGGAGGGCAATATGGAGCATGGATGGAGCTCTTGGAGCT'

print(ClumpFinding(dna, 6, 25, 5))