How to print out a 1000 new strings with a single replaced element based on a 1000-symbol string?-CodePudding

There will be a bit of molecular biology here.

So I need to generate 1000 mutant sequences bsed on a primary 1000-nucleotide sequence. Every following mutant sequence must have one random nucleotide switched to one of the same class (A to G and vice-versa; T to C and vice-versa) compared to the preceding sequence. Also, random.randint and random.seed(1) must be used.

Here's what I have so far:

import random
# below is the initial sequence
seq = 'CGCCTGTAATCCCAGCACTCTGGGAGGCAGAGGTGGGCCGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGGCAACATGGTGAAACACCATCTCTACTAAAAACACAAAAATTAGCCAGGTGTGGTGGCAGGCACCTGCAGTCCCAGCTACTCCGGAGGCTGAGGCAGGAGAATTGCTCGAACCTGGGAGGCAGGGGTTGCAGTGAGCCGACATGGCGCCACTGCACTCCAGTCTGGGCGACAGAGTGAGACCCTATCTCAAAAAAAAAAAAAAAAAAAAAAGACCCAACTCAAGTATCATCTCCAGGAAGCCTTCCCCTACTCCCAGCAATTAAATGCTCCTCAGAGAATTCCCATTTTTGGTTTACTCTTTGGTTTACCTCCAGACAGGAAGCCCCCACTGACACTGTTGTAGTCCCAGGGTGCAACACAAAGCAGAGATCACAAGCTGAGTTTAATAATTGCTTGTGGAATACATGTCCCAAGCCACCTCCTGCAGGAAGCCCTTCCAGATGCCCATTCTAGCCAGTCTGGCTCTTTGCTTCCATACCTTCACAACACTTGTGCCTCCCCCAGGGCCTCTTTCTCATCTTGCTTTCTGGGGCAGCTGTGTGCACATTTGTCTGTGTGCAGCAACTCTCTAAGGCAGGGATTTTTACTCCTATTTTTGATGAGGGGAGCTGTGGCTCAGAGAGGTTGAATAACCTAAGGCCACACAGTGAGTGGCAGAGCCAGGAATGTGACTTGGGTCCATTTGAATCCAAAGTCCCTGTACTTTCCACTGCCCTACCTAGATGTCCCTGTACCTCCTATAAAATCAGCATGGAGCCTGGTGCCTGGTAGTCCCTACAAATATTCACAAATTGGAGCTTAGCTCAGCTCTCAGGCAAGGCCCAGGTCAAAAGGGCAGATACAGCTTTGGGACCTTAGTTGCCACCACATGCCATACCTTCTTCCCAGCAGAAGGACTCCCTCCAAGACAGGGTAGGGGTGGAGG'
n = 0
while n <= 1000: # setting up a cycle for 1000 mutations
    i = random.randint(0, 1001) # choosing  random nucleotide to switch
    if seq[i] == 'A':
        print(seq.replace('A', 'G', 1)) # the third argumunt is supposed to show how many times a nucleotide must be switched but it does't work for some reason
    elif seq[i] == 'G':
        print(seq.replace('G', 'A', 1))
    elif seq[i] == 'C':
        print(seq.replace('C', 'T', 1))
    elif seq[i] == 'T':
        print(seq.replace('T', 'C', 1))
    n = n   1

The main problems I encountered is getting the program to generate new mutations based on the previous sequence, not the original one and only substituting one nucleotide.

CodePudding user response：

You need to update the sequence of nucleotides in the loop. Strings cannot be changed, so I'd recommend just using a list of letters to start:

import random

# Since string cannot be changed/mutated, 
# break up sequence into a list of strings
seq = list('CGCCTGTAATCCCAGCACTCTGGGAGGCAGAGGTGGGCCGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGGCAACATGGTGAAACACCATCTCTACTAAAAACACAAAAATTAGCCAGGTGTGGTGGCAGGCACCTGCAGTCCCAGCTACTCCGGAGGCTGAGGCAGGAGAATTGCTCGAACCTGGGAGGCAGGGGTTGCAGTGAGCCGACATGGCGCCACTGCACTCCAGTCTGGGCGACAGAGTGAGACCCTATCTCAAAAAAAAAAAAAAAAAAAAAAGACCCAACTCAAGTATCATCTCCAGGAAGCCTTCCCCTACTCCCAGCAATTAAATGCTCCTCAGAGAATTCCCATTTTTGGTTTACTCTTTGGTTTACCTCCAGACAGGAAGCCCCCACTGACACTGTTGTAGTCCCAGGGTGCAACACAAAGCAGAGATCACAAGCTGAGTTTAATAATTGCTTGTGGAATACATGTCCCAAGCCACCTCCTGCAGGAAGCCCTTCCAGATGCCCATTCTAGCCAGTCTGGCTCTTTGCTTCCATACCTTCACAACACTTGTGCCTCCCCCAGGGCCTCTTTCTCATCTTGCTTTCTGGGGCAGCTGTGTGCACATTTGTCTGTGTGCAGCAACTCTCTAAGGCAGGGATTTTTACTCCTATTTTTGATGAGGGGAGCTGTGGCTCAGAGAGGTTGAATAACCTAAGGCCACACAGTGAGTGGCAGAGCCAGGAATGTGACTTGGGTCCATTTGAATCCAAAGTCCCTGTACTTTCCACTGCCCTACCTAGATGTCCCTGTACCTCCTATAAAATCAGCATGGAGCCTGGTGCCTGGTAGTCCCTACAAATATTCACAAATTGGAGCTTAGCTCAGCTCTCAGGCAAGGCCCAGGTCAAAAGGGCAGATACAGCTTTGGGACCTTAGTTGCCACCACATGCCATACCTTCTTCCCAGCAGAAGGACTCCCTCCAAGACAGGGTAGGGGTGGAGG')

for n in range(1000):  # setting up a cycle for 1000 mutations
    i = random.randint(0, len(seq)-1)  # choosing  random nucleotide to switch

    print(i)
    print(seq[i])  # i-th nucleotide before the mutation

    if seq[i] == 'A':
        seq[i] = 'G'
    elif seq[i] == 'G':
        seq[i] = 'A'
    elif seq[i] == 'C':
        seq[i] = 'T'
    elif seq[i] == 'T':
        seq[i] = 'C'

    print(seq[i]). # i-th nucleotide after the mutation

    print(''.join(seq))  # join nucleotides into a string for printing

CodePudding user response：

random.randrange() is more appropriate to choose a random index in a fixed list, and str.maketrans() and str.translate() are a faster and more straightforward way to translate one letter to another.

Make sure to replace the character in the previous iteration each time. Strings are immutable, so use a mutable list:

import random

xlat = str.maketrans('AGCT','GATC')
#seq = list('CGCCTGTAATCCCAGCACTCTGGGAGGCAGAGGTGGGCCGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGGCAACATGGTGAAACACCATCTCTACTAAAAACACAAAAATTAGCCAGGTGTGGTGGCAGGCACCTGCAGTCCCAGCTACTCCGGAGGCTGAGGCAGGAGAATTGCTCGAACCTGGGAGGCAGGGGTTGCAGTGAGCCGACATGGCGCCACTGCACTCCAGTCTGGGCGACAGAGTGAGACCCTATCTCAAAAAAAAAAAAAAAAAAAAAAGACCCAACTCAAGTATCATCTCCAGGAAGCCTTCCCCTACTCCCAGCAATTAAATGCTCCTCAGAGAATTCCCATTTTTGGTTTACTCTTTGGTTTACCTCCAGACAGGAAGCCCCCACTGACACTGTTGTAGTCCCAGGGTGCAACACAAAGCAGAGATCACAAGCTGAGTTTAATAATTGCTTGTGGAATACATGTCCCAAGCCACCTCCTGCAGGAAGCCCTTCCAGATGCCCATTCTAGCCAGTCTGGCTCTTTGCTTCCATACCTTCACAACACTTGTGCCTCCCCCAGGGCCTCTTTCTCATCTTGCTTTCTGGGGCAGCTGTGTGCACATTTGTCTGTGTGCAGCAACTCTCTAAGGCAGGGATTTTTACTCCTATTTTTGATGAGGGGAGCTGTGGCTCAGAGAGGTTGAATAACCTAAGGCCACACAGTGAGTGGCAGAGCCAGGAATGTGACTTGGGTCCATTTGAATCCAAAGTCCCTGTACTTTCCACTGCCCTACCTAGATGTCCCTGTACCTCCTATAAAATCAGCATGGAGCCTGGTGCCTGGTAGTCCCTACAAATATTCACAAATTGGAGCTTAGCTCAGCTCTCAGGCAAGGCCCAGGTCAAAAGGGCAGATACAGCTTTGGGACCTTAGTTGCCACCACATGCCATACCTTCTTCCCAGCAGAAGGACTCCCTCCAAGACAGGGTAGGGGTGGAGG')
#mutations = 1000
seq = list('CGCCTGTAAT')
mutations = 5

random.seed(1)
for _ in range(mutations):
    i = random.randrange(len(seq))   # equivalent to random.randint(0,len(seq)-1)
    seq[i] = seq[i].translate(xlat)  # translate and replace at index
    print(''.join(seq))

Output:

CGTCTGTAAT
CGTCTGTAAC
CATCTGTAAC
CATCCGTAAC
CGTCCGTAAC