CODEWITHSUNDEEP
pythonpython-3.x
Saram
Saram

Reputation: 25

How to reverse_complementary several strings in a list

How can I get the complementary reverse for dna? following formula works for first string but when I add the second string in the list it does not work. 

dna = ['CAG', 'AGT']

def reverse_complementary (char):
    my_dictionary = {"A": "T", "C": "G", "G": "C", "T": "A"} 
    return "".join([my_dictionary[i] for i in reversed(char)])

print("reverse_complementary =" , reverse_complementary(dna))

Upvotes: 1

Views: 114

Answers (2)

Tom Zych
Tom Zych

Reputation: 13576

If you pass a str to reverse_complementary, it will reverse and translate the characters, which is what you want.

If you pass a list of str objects, as you’re doing here, it will reverse the list, then try to look up each str in the dict, and that will fail.

How to fix it? That depends on whether you want to pass single DNA sequences or lists of them. The former seems more generic, so I’ll go with that.

reverse_complementary already works with strings, so that’s unchanged. We need to call it differently:

dna = ['CAG', 'AGT']

for s in dna:
    print("reverse_complementary =" , reverse_complementary(s))

Edit: how to print results as a list.

With a loop:

lst = []
for s in dna:
    lst.append(reverse_complementary(s))
print("reverse_complementary =" , lst)

With a list comprehension:

lst = [reverse_complementary(s) for s in dna]
print("reverse_complementary =" , lst)

Upvotes: 2

MSeifert
MSeifert

Reputation: 152677

You need to perform the translation on each of your strings seperatly (and not the list itself), this can be done with a loop or with map or an explicit list-comprehension, for example:

def reverse_complementary(char):
    my_dictionary = {"A": "T", "C": "G", "G": "C", "T": "A"} 
    return ["".join([my_dictionary[i] for i in reversed(seq)]) for seq in char]

However when you want to map characters to other characters it's generally better to use str.maketrans and str.translate:

to_complement = str.maketrans({"A": "T", "C": "G", "G": "C", "T": "A"})

def reverse_complementary(char):
    return [seq[::-1].translate(to_complement) for seq in char]

The [::-1] is another (also more efficient) way of reversing a string.

Upvotes: 0

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