rosalind kmer solutions

kmer.py

#!/usr/bin/env python3.6
# sensible solution
import re
import sys
import itertools

def get_seq(path):
    """return fasta sequence from file"""
    lines = open(path).readlines()
    seq = ""
    for line in lines:
        if not line.startswith(">"):
            seq += line.strip()
    return seq

def count_kmer(kmer, seq):
    """count number of kmer in seq with overlaps"""
    return len(re.findall(f"(?={kmer})", seq))

def kmers(k=4):
    """make generator of lexicographically ordered kmers"""
    for i in itertools.product("ACGT", repeat=k):
        yield "".join(i)

def main():
    seq = get_seq(sys.argv[1])
    ans = [count_kmer(k, seq) for k in kmers()]
    print(*ans)

if __name__ == "__main__":
    main()

kmer_code_golf.py

#!/usr/bin/env python3.6
from re import findall
from sys import argv
from itertools import product

seq = "".join(i.strip() for i in open(argv[1]).readlines()[1:])
all_kmers = ["".join(j) for j in product("ACGT", repeat=4)]
print(*map(lambda kmer: len(findall(f"(?={kmer})", seq)), all_kmers))