Check if a string contains a string except a list

Question

I have a string as follows:

f = 'ATCTGTCGTYCACGT'

I want to check whether the string contains any characters except: A, C, G or T, and if so, print them.

for i in f:                                                                                                                        
    if i != 'A' and i != 'C' and i != 'G' and i != 'T':                                                                             
        print(i)

Is there a way to achieve this without looping through the string?

Do you want to check if the characters are not in the string, or do you want to print all the characters except for some characters? these are 2 different tasks — DeepSpace
– DeepSpace, Commented Jan 21, 2020 at 18:37
I want to know if there is any character in the f string except 'A', 'C', 'G' or 'T'. If so, I want to print it. — Homap
– Homap, Commented Jan 21, 2020 at 18:45
Is your main reason for not wanting a loop the time/efficiency? Sets seem like a good place to optimize a lookup, but at the cost of the conversion of a string to a set, which can have a significant processing overhead — G. Anderson
– G. Anderson, Commented Jan 21, 2020 at 18:52
Does this answer your question? Check if a string contains only given characters — Georgy
– Georgy, Commented Jan 21, 2020 at 19:07
Do you mean without using a for loop, or any looping construct. For example, under the hood, functional programming methods (any, map), and it could be argued that regex does as well. For clarity do you want to avoid any function that employs a looping construct, or avoid the basic looping functions, such as for, while, etc ? If the former, perhaps set, for the latter, I'd probably take a regex (match) approach. — SherylHohman
– SherylHohman, Commented Jan 21, 2020 at 20:02

Ch3steR · Accepted Answer · 2020-01-21 19:05:25Z

3

You can use set to achieve the desired output.

f = 'ATCTGTCGTYCACGTXYZ'
not_valid={'A', 'C', 'G' , 'T'}
unique=set(f)
print(unique-not_valid)

output

{'Y','X','Z'} #characters in f which are not equal to 'A','C','G','T'

edited Jan 21, 2020 at 19:05

answered Jan 21, 2020 at 18:52

Ch3steR

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4 Comments

DeepSpace Over a year ago

Correct if OP does not care about order or duplication (should f = 'ABCA' ; not_valid = {'A'} print A or AA)?

Ch3steR Over a year ago

@DeepSpace Sorry, I didn't understand your query (should f = 'ABCA' ; not_valid = {'A'} print A or AA)? If you don't mind can you explain again?

DeepSpace Over a year ago

If there are duplicated missing characters your solution will only print one of them, and also out of order (because sets are unordered). I'm not saying that it is bad, just that OP didn't specify what they want

Ch3steR Over a year ago

@DeepSpace My first approach was using regex but in one of the comments OP mentioned this I want to know if there is any character in the f string except 'A', 'C', 'G' or 'T' So, I thought set is one of the option.

DeepSpace · Accepted Answer · 2020-01-21 18:52:41Z

3

Depending on the size of your input string, the for loop might be the most efficient solution.

However, since you explicitly ask for a solution without an explicit loop, this can be done with a regex.

import re

f = 'ABCDEFG'

print(*re.findall('[^ABC]', f), sep='\n')

Outputs

D
E
F
G

edited Jan 21, 2020 at 18:52

answered Jan 21, 2020 at 18:51

DeepSpace

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Comments

Kumpelinus · Accepted Answer · 2020-01-21 18:49:16Z

0

Just do

l = ['A', 'C', 'G', 'T']

for i in f:
    if i not in l:
        print(i)

It checks whether the list contains a char of the list

If you don't want to loop through the list you can do:

import re

l = ['A', 'C', 'G', 'T']

contains = bool(re.search("%s" % "[" + "".join(l) + "]", f))

edited Jan 21, 2020 at 18:49

answered Jan 21, 2020 at 18:38

Kumpelinus

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2 Comments

DeepSpace Over a year ago

"Is there a way to achieve this without looping through the string?" This code does exactly what OP's does, just in a neater way (which wasn't the premise of the question)

Kumpelinus Over a year ago

That is right. I have edited it so that it now meets the requirements

badger0053 · Accepted Answer · 2020-01-21 18:57:06Z

0

Technically this loops but we convert your input string to a set which removes duplicate values

accepted_values = ['a','t','c','g']

input = 'ATCTGTCGTYCACGT'

print([i for i in set(input.lower()) if i not in accepted_values])

answered Jan 21, 2020 at 18:57

badger0053

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1 Comment

Kumpelinus Over a year ago

I also thought about that but i did not know if this counts as "looping"

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