random mutation in a DNA sequence - mutation rate in python

Question

EDITED

I created a function that introduces random mutations with a determined mutation rate (example 0.05).

input='ATCTAGGAT'


def mutate_v2(sequence, mutation_rate):
    dna_list = list(sequence)
    for i in range(len(sequence)):
        r = random.random()
        if r < mutation_rate:
            mutation_site = random.randint(0, len(dna_list) - 1)
            print(mutation_site)
            dna_list[mutation_site] = random.choice(list('ATCG'))
        return ''.join(dna_list)


## run the function
mutate_v2(input, 0.01)

Now I want the function to take as input a list of sequences (example: list_sequences = ['ATTCTGTA', 'TTCGCTAA', 'ACCCGCTA']) and return each mutated sequence (in a list: output).

Any help please!

Thanks

What exactly is mutation rate? If you're getting the same input sequence, it's probably because `r` is never below 0.01? — not_speshal, Oct 14 '21 at 19:04
The probability of the draw being below 0.01 in just 9 tries is too low, that's why you're not observing mutations, just to convince you, try with r=0.5 — Ultramoi, Oct 14 '21 at 19:05
@Ultramoi I edited the question, can you please help to get result for a list of sequences instead of juste one. Thanks — , Oct 14 '21 at 19:59

Timur Shtatland · Accepted Answer · 2021-10-15T14:24:19.377

2

I would keep the interface of mutate_v2 the same (I think the interface is OK the way it is), but call it using list comprehension, like so:

input = [seq_1, seq_2, seq_n]
mutated_input = [mutate_v2(s) for s in input]

Alternatively, you can wrap it into its own method like so:

def mutate_multiple(sequences):
    return [mutate_v2(s) for s in sequences]

# call the method:
input = [seq_1, seq_2, seq_n]
mutated_input = mutate_multiple(input)

edited Oct 15 '21 at 14:24

answered Oct 14 '21 at 21:49

Timur Shtatland

12,024
2
30
47

@Ab_Lh : Updated the answer by adding a wrapper method. – Timur Shtatland Oct 15 '21 at 14:25

score 1 · Answer 2 · answered Oct 14 '21 at 20:26

1

To return a list of sequences instead of just one, you simply have to call you function multiple times.

def multiple_draws(sequence, mutation_rate, n_draws=1):
    return [mutate_v2(sequence, mutation_rate) for _ in range (n_draws)]

print(multiple_draws(input, 0.01, 10)

And if it's easier to read for you:

def multiple_draws(sequence, mutation_rate, n_draws=1):
    mutations = []
    for _ in range(n_draws):
       mutation = mutate_v2(sequence, mutation_rate)
       mutations.append(mutation)
    return mutations

answered Oct 14 '21 at 20:26

Ultramoi

166
1
9

Thank you for your effort. But I'm looking for a function that accepts as input a list of sequences and not only one. for example **input=[seq_1, seq_2, seq_n]**, then it returns a new list **output=[seq_1_muted, seq_2_muted, seq_n_muted]** . – Oct 14 '21 at 20:41
1

I see, then I think the answer from Timur Shtatland should fit your expectations :) – Ultramoi Oct 15 '21 at 11:24

random mutation in a DNA sequence - mutation rate in python

EDITED

2 Answers2