Using python replace function in for loop

Question

I'm trying to test out changing certain bases in a DNA sequence, but the way I have it written now is mutating all the bases of the same kind (i.e.: all 'A's to 'G's) instead of only changing the bases within the section of DNA I want to mutate.

I know this is because of how I have my replace function input set up, but I'm not sure how to specify which base I want changed based on the for loop - whichever base is targeted in each iteration of the for loop is the only one I want to mutate within that iteration. Here's what I have currently:

import random
word = 'GTGATCCAGT'

for base in word[5:]:
    print base
    if base == 'A':
        new_base = random.choice('CTG')
        print new_base
        new_word = word.replace(base, new_base)
        print new_word
    elif base == 'C':
        new_base = random.choice('ATG')
        print new_base
        new_word = word.replace(base, new_base)
        print new_word
    elif base == 'G':
        new_base = random.choice('CTA')
        print new_base
        new_word = word.replace(base, new_base)
        print new_word
    elif base == 'T':
        new_base = random.choice('AGC')
        print new_base
        new_word = word.replace(base, new_base)
        print new_word
    word = new_word

Thank you!

jonrsharpe · Accepted Answer · 2014-07-10 10:43:22Z

1

There is a lot of duplication in your code. I would suggest:

import random

word = list('GTGATCCAGT')
BASES = "ACGT"

for index, base in enumerate(word[:5]):
    word[index] = random.choice(BASES.replace(base, ""))

word = "".join(word)

A trial run gives me:

>>> word
'TACTACCAGT'

Note the switch to a list - strings in Python are immutable, so you can't (easily) change an individual character. By contrast, lists are mutable, so you can switch the item at a given index without any fuss.

answered Jul 10, 2014 at 10:43

jonrsharpe

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Comments

lvc · Accepted Answer · 2014-07-10 10:52:45Z

Your loop doesn't currently have enough information to do what you want: in particular, it doesn't know which base you are currently looking at, only what its value is. You could use the builtin enumerate to introduce that information, but a simpler way would be to change the logic so it doesn't rebuild the string each time - instead, write a generator that gives you each successive new_base, and join them all into new_word at the end. It looks like this:

def rebase(word):
    for base in word:
        print base
        if base == 'A':
           new_base = random.choice('CTG')
           print new_base
           yield new_base
        # etc
        else:
          # If you didn't change this base, yield the original one
          yield base

 new_word = word[:5] + ''.join(rebase(word[5:]))

You might also want to use a dictionary to avoid the chain of ifs - like this:

def rebase(word):
    possible_replacements = {'A': 'CTG', 'C': 'ATG'} # etc
    for base in word:
        print base
        try:
           yield random.choice(possible_replacements[base])
        except KeyError:            
          # If you didn't change this base, yield the original one
          yield base

new_word = word[:5] + ''.join(rebase(word[5:]))

ruthless · Accepted Answer · 2014-07-10 10:43:20Z

0

When you are looping through the sequence, make sure to keep an index as well. This index will help you determine the location in the string that you want to replace. When you want to add contents to a location, simply split the string at that location into two strings. Then concatenate the new string by adding it in the middle of the two strings and thus you end up with a new string with the correct contents.

edited Jul 10, 2014 at 10:43

answered Jul 10, 2014 at 10:32

ruthless

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2 Comments

jonrsharpe Over a year ago

You can't alter strings by changing the character at a given index - they are immutable.

ruthless Over a year ago

Sorry. I meant to concatenate the string prior to the index location with the new contents at that location, and the rest of the string after that location. I'll fix my answer

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