dna manipulation functions

dna_functions.py

from itertools import product
from functional import seq

def all_kmers(k):
  '''return list of all dna carthesien products of length k'''
  all = list(product('ACGT', repeat=k))
  return seq(all).map(lambda x: ''.join(x)).to_list()
  
def kmer_per_segment(dna_segment, k):
  '''return all the dna substrings of length k of the different dna strings in dna list'''
  return [dna_segment[i:i+k] for i in range(len(dna_segment)-(k-1))]

def median_distance(dna, k, list_kmers):
  '''return the first substring of length k encounters with the lowest substring/dna distance'''
    distance = float('inf')
    median = (str)
    for kmer in all_kmers(k):
        sum_distance = 0
        for i in dna:
            distance_per_kmer = float('inf')
            for mer in kmer_per_segment(i, k):
                d = lv.distance(mer,kmer)
                if distance_per_kmer > d:
                    distance_per_kmer = d
            sum_distance += distance_per_kmer
        if distance > sum_distance:
            distance = sum_distance
            median = kmer
    return distance, median