Replace a list or string element with a random one..

Replace a list or string element with a random one.. - Printable Version

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Replace a list or string element with a random one.. - pianistseb - May-09-2019

Hello!

I have to do a very simple task, but I have problems with speed. I have a list called 'chromosome', and I want to replace each N into A,G,C or T at random. I made this code, which is very slow (chromosome in this code is a list):

for i in range(0,len(chromosome)):
    if (chromosome[i] is not ('A' or 'C' or 'G' or 'T')):
        r=rd.randint(1,4)
        if r==1:
            chromosome[i]='A'
        elif r==2:
            chromosome[i]='G'
        elif r==3:
            chromosome[i]='C'
        else:
            chromosome[i]='T'

Can I do something to make it run faster?

Thank you!

RE: Replace a list or string element with a random one.. - buran - May-09-2019

First of all let's fix a bug in your code. You will be surprised to learn that

    if (chromosome[i] is not ('A' or 'C' or 'G' or 'T')):

doesn't do what you expect. see for yourself:

chromosomes = 'NACGT'
for chromosome in chromosomes:
    print(chromosome, chromosome is not ('A' or 'C' or 'G' or 'T'))

Output:N True
A False
C True
G True
T True

so you replace everything that is not A

you have two alternatives

if chromosome == 'N': # replace just N

if chromosome not in 'ACGT': # replace everything that is not A, C, G or T

if chromosome not in ['A', 'C', 'G', 'T']: # replace everything that is not A, C, G or T

something like this

import random
chromosomes = ['N', 'A', 'C', 'G', 'N', 'T']
new_chromosomes = [random.choice('ACGT') if c == 'N' else c for c in chromosomes]
print(new_chromosomes)

Output:
['A', 'A', 'C', 'G', 'C', 'T']

RE: Replace a list or string element with a random one.. - pianistseb - May-09-2019

Thank you very much for your solution! I didn't put 'if is equal to N' because sometimes in chromosomes you can find also other letters like R or M. Your code is really simple and efficient!

RE: Replace a list or string element with a random one.. - buran - May-09-2019

(May-09-2019, 08:21 AM)pianistseb Wrote: I didn't put 'if is equal to N' because sometimes in chromosomes you can find also other letters like R or M.

do you want to replace these? if you want to replace everything not in ACGT, then use any of the other two example conditions