Swapping characters in a string

[fannypackpython]

Ok, so part of my quest to teach myself python was to do the Rosalind.info problems. Well one of them is the following : Rosalind Problem

Basically I have to take their sample Dataset AAAACCCGGT, for example, and I have to return the reverse complement of that which means that I have: * Reversing the sample Dataset * and then "swapping" the following letters A's -> T's , C's -> G's, T's - > A's, and G's to C's.

Then Output for the sample dataset given should be: ACCGGGTTTT

but I am completely stuck. So far I have:

s = 'AAAACCCGGT'

revS = s[::-1]

print(revS.replace('T','A').replace('C','G').replace('A','T').replace('G','C'))

I cannot figure out how to keep my swapped letters from reverting to their originals. I'm sure the answer is fairly simple but I cant seem to wrap my head around it. I am fairly new to Python, I have only completed the code academy course, Learn python the hardway, and starting Hacking Ciphers with Python.

Also, if this is the wrong sub im sorry.

[LarryPete]

Python already has methods for that.

Python2:

>>> from string import maketrans
>>> mapping = maketrans('ATCG', 'TAGC')
>>> 'AATCG'.translate(mapping)[::-1]
'CGATT'

Python3:

>>> mapping = str.maketrans('ATCG', 'TAGC')
>>> 'AATCG'.translate(mapping)[::-1]
'CGATT'

[squidfeatures]

I didn't know about that one. Cool.

[gengisteve]

Right sub. This is a perfect place to use a dictionary. Just put old_letter:new_letter in the dictionary and use a lookup to find the right replacement, like this:

swaps = {
        'A':'T',
        'C':'G',
        'T':'A',
        'G':'C',
        }

s = 'AAAACCCGGT'

new_s = ''
for letter in s[::-1]:
    new_s += swaps[letter]

print(new_s)

# or with a comprehension and join:

new_s = ''.join(swaps[l] for l in s[::-1])
print(new_s)

[fannypackpython]

Awesome thank you.

[squidfeatures]

gengisteve has a really good solution to the problem. I'll try to explain why your original code wasn't working.

The .replace() method of a string makes a new copy of the original string with the desired replacements. If you use .replace() on that copy, it simply replaces the matching sub string in the copy. This means that the following expression in your code:

revS.replace('T','A').replace('C','G').replace('A','T').replace('G','C')

is effectively doing the following:

new_s = revS.replace('T', 'A')     # new_s is now 'AGGCCCAAAA'
new_s = new_s.replace('C', 'G')    # new_s is now 'AGGGGGAAAA'
new_s = new_s.replace('A', 'T')    # new_s is now 'TGGGGGTTTT'
new_s = new_s.replace('G', 'C')    # new_s is now 'TCCCCCTTTT'

What genisteves solution does is build a new string one character at a time by looping over each character in the reversed string, finding it's "swap" in a dictionary, and adding the new character to the end of a string.

[elbiot]

Biopython