CODEWITHSUNDEEP
pythonbioinformaticsdna-sequencegenetics
user8769986
user8769986

Reputation:

random mutation in a DNA sequence - mutation rate in python

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

Upvotes: 2

Views: 1090

Answers (2)

Timur Shtatland
Timur Shtatland

Reputation: 12347

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)

Upvotes: 2

Ultramoi
Ultramoi

Reputation: 213

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

Upvotes: 1

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