rna_codon_tbl = {'UUU': 'F', 'CUU': 'L', 'AUU': 'I', 'GUU': 'V',
                 'UUC': 'F', 'CUC': 'L', 'AUC': 'I', 'GUC': 'V',
                 'UUA': 'L', 'CUA': 'L', 'AUA': 'I', 'GUA': 'V',
                 'UUG': 'L', 'CUG': 'L', 'AUG': 'M', 'GUG': 'V',
                 'UCU': 'S', 'CCU': 'P', 'ACU': 'T', 'GCU': 'A',
                 'UCC': 'S', 'CCC': 'P', 'ACC': 'T', 'GCC': 'A',
                 'UCA': 'S', 'CCA': 'P', 'ACA': 'T', 'GCA': 'A',
                 'UCG': 'S', 'CCG': 'P', 'ACG': 'T', 'GCG': 'A',
                 'UAU': 'Y', 'CAU': 'H', 'AAU': 'N', 'GAU': 'D',
                 'UAC': 'Y', 'CAC': 'H', 'AAC': 'N', 'GAC': 'D',
                 'UAA': 'Stop', 'CAA': 'Q', 'AAA': 'K', 'GAA': 'E',
                 'UAG': 'Stop', 'CAG': 'Q', 'AAG': 'K', 'GAG': 'E',
                 'UGU': 'C', 'CGU': 'R', 'AGU': 'S', 'GGU': 'G',
                 'UGC': 'C', 'CGC': 'R', 'AGC': 'S', 'GGC': 'G',
                 'UGA': 'Stop', 'CGA': 'R', 'AGA': 'R', 'GGA': 'G',
                 'UGG': 'W', 'CGG': 'R', 'AGG': 'R', 'GGG': 'G'}

# DNA
from collections import Counter

with open("rosalind_dna.txt", 'r') as f:
  file = f.readline()

Counter(sorted(file))

# RNA

from collections import Counter

with open("rosalind_rna.txt", 'r') as f:
  file = f.readline()

Counter(file.replace('T', 'U').strip())

# REVC

with open("rosalind_revc.txt", 'r') as f:
  file = f.readline().strip()

mapping = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
file_reversed = file[::-1]
solution = ''.join([mapping[letter] for letter in file_reversed])

# fib

def fib(n, k):

    if n == 0: return 0
    if n == 1: return 1

    return fib(n-1, k) + k*fib(n-2, k)

with open("rosalind_fib.txt", 'r') as f:
  file = f.readline().strip()

fib(int(file.split()[0]), int(file.split()[1]))

# gc

import numpy as np

with open("rosalind_gc.txt", 'r') as f:
  file0 = f.read()

file1 = file0.split('>')[1:]
file2 = [f.strip().split('\n') for f in file1]
file3 = {f[0]: ''.join(f[1:]) for f in file2}
file4 = {f[0]: 100*np.mean([1 if x in ['C', 'G'] else 0 for x in f[1]]) for f in file3.items()}

for x in list(sorted(file4.items(), key = lambda x: x[1])[-1]): print(x)

# hamm

with open("rosalind_hamm.txt", 'r') as f:
  file = f.read()

f = file.strip().split('\n')
sum([1 if f[0][i] != f[1][i] else 0 for i in range(len(f[0]))])

# iprb

from itertools import product, combinations
import numpy as np

with open("rosalind_iprb.txt", 'r') as f:
    file = f.read()

inds = [int(i) for i in file.replace('\n', '').split(' ')]
genes = [['Y', 'Y'], ['Y', 'y'], ['y', 'y']]
pop = sum([[genes[i]]*inds[i] for i in range(3)], [])

combs = list(combinations(pop, 2))
children = sum([list(product(*comb)) for comb in combs], [])
result = np.mean([1 if 'Y' in child else 0 for child in children])
result

# prot
with open("rosalind_prot.txt", 'r') as f:
  file = f.read()

s = file
r = list(range(0, len(s) + 1, 3))
t = [s[r[i]:r[(i+1)]] for i, _ in enumerate(r[:-1])]
''.join([rna_codon_tbl[snippet] for snippet in t]).replace('Stop', '')

# subs
import re

with open("rosalind_subs.txt", 'r') as f:
  file = f.readlines()

file1 = [f.strip() for f in file]
s, t = file1[0], file1[1]
for i in [(m.start() + 1) for m in re.finditer('(?={})'.format(t), s)]: print(i, end = " ")