Reverse complement DNA

Question

I have this equation for reverse complementing DNA in python:

def complement(s): 
    basecomplement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'} 
    letters = list(s) 
    letters = [basecomplement[base] for base in letters] 
    return ''.join(letters)
def revcom(s):
    complement(s[::-1])
print("ACGTAAA")
print(complement("ACGTAAA"[::-1]))
print(revcom("ACGTAAA"))

however the lines:

print(complement("ACGTAAA"[::-1]))
print(revcom("ACGTAAA"))

do not equal one another. only the top line gives an answer. the bottom just prints "NONE"

any help why this is?

I bet it prints `None`, not `"NONE"`. That's actually an important distinction. Remember, when asking for help with debugging, it is important to report the error *exactly* as it occurs. — SethMMorton, Oct 24 '13 at 17:24

mdml · Answer 1 · 2013-10-24T18:18:07.747

7

You forgot the return statement in revcom. Try this:

def revcom(s):
    return complement(s[::-1])

If you don't explicitly return a value from a function in Python, then the function returns None.

edited Oct 24 '13 at 18:18

answered Oct 24 '13 at 15:58

mdml

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corinna · Answer 2 · 2016-07-12T11:20:31.380

6

Python3, including whole IUPAC alphabet for nucleotides:

def revcomp(seq):
    return seq.translate(str.maketrans('ACGTacgtRYMKrymkVBHDvbhd', 'TGCAtgcaYRKMyrkmBVDHbvdh'))[::-1]

In Python2:

from string import maketrans

def revcomp(seq):
    return seq.translate(maketrans('ACGTacgtRYMKrymkVBHDvbhd', 'TGCAtgcaYRKMyrkmBVDHbvdh'))[::-1]

edited Jul 12 '16 at 11:20

answered Jul 12 '16 at 10:59

corinna

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score 4 · Answer 3 · answered Jul 19 '14 at 22:46

4

A pretty one liner to reverse complement a DNA sequence:

revcompl = lambda x: ''.join([{'A':'T','C':'G','G':'C','T':'A'}[B] for B in x][::-1])
print revcompl("AGTCAGCAT")

answered Jul 19 '14 at 22:46

xApple

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score 1 · Answer 4 · answered Oct 24 '13 at 15:58

1

You need to return the result from revcom().

answered Oct 24 '13 at 15:58

Christian Ternus

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score 0 · Answer 5 · answered Aug 24 '15 at 07:31

0

`a = "AAAACCCGGT"
a= a[::-1]
print("reverse: "+a)
a = a.replace('A','a')
a = a.replace('T','A')
a = a.replace('a','T')
a = a.replace('C','c')
a = a.replace('G','C')
a = a.replace('c','G')
print("complement : "+a)`

answered Aug 24 '15 at 07:31

Shahadat Hossain

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Reverse complement DNA

5 Answers5