Generating complementary DNA sequence

Question

I am still relatively new to Python but I have been actively doing sample examples to try and get used to problem solving aspect of programming.

With that said, I stumbled upon a question that asks you to write a code to convert DNA strand to its complementary form.

What I have written works, but I don't believe that my approach is efficient enough. Could you please review my code and guide me as to how I might improve on it? I feel like there will be a faster way than writing multiple if, elif statements.

import sys

def check_input(user_input):
    if len(user_input) == 0:
        sys.exit("No strand provided.")
    return user_input

def complementary(strand):
    complementary_strand = ''
    for dna in strand:
        if dna == 'A':
            complementary_strand += 'T'
        elif dna == 'a':
            complementary_strand += 't'
        elif dna == 'T':
            complementary_strand += 'A'
        elif dna == 't':
            complementary_strand += 'a'
        elif dna == 'G':
            complementary_strand += 'C'
        elif dna == 'g':
            complementary_strand += 'c'
        elif dna == 'C':
            complementary_strand += 'G'
        elif dna == 'c':
            complementary_strand += 'g'
        else:
            complementary_strand += 'x'
    return complementary_strand

if __name__ == "__main__":
    user_input = input("Enter strand: ")
    print()
    strand = check_input(user_input)
    complementary_strand = complementary(strand)
    print("Complementary strand is {}".format(complementary_strand))

200_success · Accepted Answer · 2018-05-06 01:29:40Z

Typically, a character-for-character replacement is best done using str.translate():

strand.translate(str.maketrans('AaTtGgCc', 'TtAaCcGg'))

However, your situation is trickier, because you also want to map all invalid characters to 'x'. To achieve that, you would need to read the str.maketrans() documentation carefully, and figure out that you can wrap the mapping in a collections.defaultdict.

from collections import defaultdict

DNA_COMPLEMENTS = defaultdict(lambda: 'x', str.maketrans('AaTtGgCc', 'TtAaCcGg'))

def complementary(strand):
    return strand.translate(DNA_COMPLEMENTS)

Note that lambda: 'x' is a way to make a function that, when called with no parameters, returns the letter 'x'.

samman · Accepted Answer · 2020-07-03 18:52:26Z

I know this is old, but considering the amount of views it gets (and I also looked it up now) thought I'd also add.

Couldn't you just use a dictionary, and convert all letters to upper (this way you don't have to import anything either)?

DNA_complement_dict={'A':'T',
                     'T':'A',
                     'G':'C',
                     'C':'G'

def check_input(user_input):
    if len(user_input) == 0:
        sys.exit("No strand provided.")
    return user_input.upper()

def complementary(strand):
    complementary_strand = ''
    for dna in strand:
       try:
         complementary_strand += DNA_complement_dict[dna]
       except:
         complementary_strand += 'X'
    return complementary strand

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