Exercise 1 solution

B = "TCAG"
AA = "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
CODON = {a + b + c: AA[16 * i + 4 * j + k]
         for i, a in enumerate(B) for j, b in enumerate(B) for k, c in enumerate(B)}

def translate(dna):
    protein = []
    for i in range(0, len(dna) - 2, 3):
        aa = CODON[dna[i:i + 3]]
        if aa == "*":
            break
        protein.append(aa)
    return "".join(protein)

def classify(old, new):
    if len(old) != len(new):
        return "frameshift" if (len(new) - len(old)) % 3 else "in-frame indel"
    a, b = translate(old), translate(new)
    if a == b:
        return "silent"
    return "nonsense" if len(b) < len(a) else "missense"

def find_orfs(dna):
    found = []
    for s in range(len(dna) - 2):
        if dna[s:s + 3] == "ATG":
            p = translate(dna[s:])
            end = s + 3 * len(p)
            if end + 3 <= len(dna) and CODON[dna[end:end + 3]] == "*":
                found.append((s, p))
    return found

for s in ("ATGAAATTTGGGTAA", "ATGTGGTGA", "GGATGCCCTAGATGAAATAG"):
    print(s, find_orfs(s))

Output:

ATGAAATTTGGGTAA [(0, 'MKFG')]
ATGTGGTGA [(0, 'MW')]
GGATGCCCTAGATGAAATAG [(2, 'MP'), (11, 'MK')]

Reading it: Each ATG is checked as a possible start; translate stops at the first stop codon, so a start with no stop before the end of the sequence is rejected. Nested starts in the same frame, or overlapping ones, are reported separately.