20. k-mer Composition

#!/usr/bin/env python

#PROBLEM
#============
#For a fixed positive integer k, order all possible k-mers taken from an underlying alphabet lexicographically.

#Then the k-mer composition of a string s can be represented by an array A for which A[m] denotes the number of times that the mth k-mer (with respect to the lexicographic order) appears in s.

#Given: A DNA string s in FASTA format (having length at most 100 kbp).
#Return: The 4-mer composition of s.

#Sample Dataset
#>Rosalind_6431
#CTTCGAAAGTTTGGGCCGAGTCTTACAGTCGGTCTTGAAGCAAAGTAACGAACTCCACGGCCCTGACTACCGAACCAGTTGTGAGTACTCAACTGGGTGAGAGTGCAGTCCCTATTGAGT
#TTCCGAGACTCACCGGGATTTTCGATCCAGCCTCAGTCCAGTCTTGTGGCCAACTCACCAAATGACGTTGGAATATCCCTGTCTAGCTCACGCAGTACTTAGTAAGAGGTCGCTGCAGCG
#GGGCAAGGAGATCGGAAAATGTGCTCTATATGCGACTAAAGCTCCTAACTTACACGTAGACTTGCCCGTGTTAAAAACTCGGCTCACATGCTGTCTGCGGCTGGCTGTATACAGTATCTA
#CCTAATACCCTTCAGTTCGCCGCACAAAAGCTGGGAGTTACCGCGGAAATCACAG
#Sample Output
#4 1 4 3 0 1 1 5 1 3 1 2 2 1 2 0 1 1 3 1 2 1 3 1 1 1 1 2 2 5 1 3 0 2 2 1 1 1 1 3 1 0 0 1 5 5 1 5 0 2 0 2 1 2 1 1 1 2 0 1 0 0 1 1 3 2 1 0 3 2 3 0 0 2 0 8 0 0 
#1 0 2 1 3 0 0 0 1 4 3 2 1 1 3 1 2 1 3 1 2 1 2 1 1 1 2 3 2 1 1 0 1 1 3 2 1 2 6 2 1 1 1 2 3 3 3 2 3 0 3 2 1 1 0 0 1 4 3 0 1 5 0 2 0 1 2 1 3 0 1 2 2 1 1 0 3 0 
#0 4 5 0 3 0 2 1 1 3 0 3 2 2 1 1 0 2 1 0 2 2 1 2 0 2 2 5 2 2 1 1 2 1 2 2 2 2 1 1 3 4 0 2 1 1 0 1 2 2 1 1 1 5 2 0 3 2 1 1 2 2 3 0 3 0 1 3 1 2 3 0 2 1 2 2 1 2 
#3 0 1 2 3 1 1 3 1 0 1 1 3 0 2 1 2 2 0 2 1 1

#============
#CODE

def main():
    fastaseq = parse_sequence()
    kmers_dictionary = get_kmers()
    fragmentsofDNA = DNAcutter(fastaseq)
    counter = count_kmers(kmers_dictionary, fragmentsofDNA)

def parse_sequence():
    from Bio import SeqIO
    
    file_name = input("Enter your file name (format file_name.fasta): ")

    for seq_record in SeqIO.parse(file_name, "fasta"):
        
        fastaseq = seq_record.seq

    return fastaseq
def get_kmers():
    nucleotides = ["A", "C", "G", "T"]
    kmers = []
    
    for nt1 in nucleotides:
        for nt2 in nucleotides:
            for nt3 in nucleotides:
                for nt4 in nucleotides:
                    #print(nt1, nt2, nt3, nt4)
                    kmer = [nt1+nt2+nt3+nt4]
                    kmers.extend(kmer)
    print(kmers)
    return kmers

def DNAcutter(fastaseq):
    DNA_sequence = fastaseq
    substrings = []
    for k in range(0, len(DNA_sequence)):
        fragment = DNA_sequence[k:k+4]
        substrings.append(fragment)
    print(substrings)
    return substrings

def count_kmers(kmers_dictionary, fragmentsofDNA):
    for kmer in kmers_dictionary:
        count = 0
        for fragment in fragmentsofDNA:
            if kmer == fragment:
                count +=1
        print(count, " ", end="")
    


main()