Exercise 3 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 report(orig, mut):
    a, b = translate(orig), translate(mut)
    first = "none"
    for i in range(max(len(a), len(b))):
        if a[i:i + 1] != b[i:i + 1]:
            first = i + 1
            break
    print(a, "->", b, classify(orig, mut), "first difference:", first)

orig = "GTGCACCTGACTCCTGAGGAGAAG"
report(orig, orig[:15] + "GTG" + orig[18:])
report(orig, orig[:17] + "A" + orig[18:])
report(orig, orig[:15] + orig[16:])
report(orig, orig[:15] + "TAG" + orig[18:])

Output:

VHLTPEEK -> VHLTPVEK missense first difference: 6
VHLTPEEK -> VHLTPEEK silent first difference: none
VHLTPEEK -> VHLTPRR frameshift first difference: 6
VHLTPEEK -> VHLTP nonsense first difference: 6

Reading it: The frameshift variant is compared position by position, and a protein that is shorter simply has no letter there, so the first difference is found where it ends or changes.