Reverse complement of a DNA string

Question

I have a function in python where I want the reverse complement of a DNA string.

This is what I have now:

def inversComplement(input):
    output = ''
    for letter in input:
        letter = letter.upper()

        if letter == 'A':
            output += 'T'
        elif letter == 'T':
            output += 'A'
        elif letter == 'G':
            output += 'C'
        else:
            output += 'G'

    return(output[::-1])

I was thinking of using the string.replace() method. But the problem was that if I use this the T-> A would be changed afterwards with the A -> T replacement

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

Answer 1

Yesterday I came across this presentation on YouTube with this solution using list comprehension and the join method:

def reverse_complement(dna):
    complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
    return ''.join([complement[base] for base in dna[::-1]])

Answer 2

You can do this with str.translate, which was changed slightly in Python 3. All you need to do is pass it a translation table, and it'll do what your above code is doing. However to build the translation table is hard in Python 2 and requires the helper function string.maketrans, which was changed to str.maketrans in Python 3.

But here is how you'd use it in Python 2:

>>> import string
>>> trans = string.maketrans('ATGC', 'TACG')
>>> 'ATTAGCC'.translate(trans)
'TAATCGG'

And here is how you can use it in Python 3:

>>> trans = str.maketrans('ATGC', 'TACG')
>>> 'ATTAGCC'.translate(trans)
'TAATCGG'
>>> trans = {ord('A'): 'T', ord('T'): 'A', ord('G'): 'C', ord('C'): 'G'}
>>> 'ATTAGCC'.translate(trans)
'TAATCGG'

You can re-implement this yourself, but the above is written in C, and so should out perform any Python code.

Answer 3

A quick caution on the solutions proposed in other answers. The translation table approach doesn't work because it's answering a slightly different question.

The REVERSE complement of ACGT is ACGT not TGCA. Because when you do a reverse complement you have to start by complementing item -1 then -2 etc. Rather than item 0 then 1 etc.

If you run proposed solutions you'll see they produce different answers.

>>> EX_STR="ACGT"

>>> ### Option 1 Correct
>>> def reverse_complement(dna): 
>>>     complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'} 
>>>     return ''.join([complement[base] for base in dna[::-1]])
>>> print reverse_complement(EX_STR)
ACGT

>>> ### Option 2 Incorrect
>>> import string 
>>> trans = string.maketrans('ATGC', 'TACG')
>>> print EX_STR.translate(trans)
TGCA

Answer 4

You can in fact use this method:

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

You just need to replace the uppercase letters by lowercase letters and make them uppercase again after that:

a=string.replace('A','t').replace('T','a').replace('G','c').replace('C','g')
a.upper()

It's maybe not the best way but it's easy and it works.

Answer 5

I have found a solution with the string.replace() method!

def inversComplement(input):
    return(input.upper().replace('A', 'temp').replace('T', 'A').replace('temp', 'T').replace('G', 'temp').replace('C','G').replace('temp','C')[::-1])