Read DNA sequence from FASTA rising a subclass?

Question

[Gonçalo]

Hello everyone,

I am supposed to write a function that takes a name of a file (FASTA) as an argument. When passed the name of the file, the function should read the file, discard the header and return the sequence as a string. Now, I am being asked to rise a predefined (subclass?) (defined before my code) if the sequence part of the file contains characters that are not of the letters A,C,T,G,U. Also, all U nucleotides should be replaced by T in the returned string. I think I am on the right track but have no idea how to incorporate this subclass in my code if any of the letters are not A,C,T,G,U. I am working with a small file before defining the function but this is what I have got:

This is defined before my code:

# Run this cell to define the exception
class BadSequenceException(Exception):
    pass

#my code:
file = open("sequence1.fasta")
all_lines = file.readlines()

sequences = []

with open('sequence1.fasta', 'r') as seq:
    sequence = ''

for line in seq:
    if line.startswith('>'):
        sequences.append(sequence)
        sequence = ''
    else:
        sequence += line.strip()

def check (sequence, code="ATGCU"):
    for x in sequence:
        if x not in code:
            return False

return sequence.replace("U","T")

check(sequence)

I presume that the subclasse must be raised where the RETURN FALSE is?

Also, BadSequenceException is a subclass of the class Exception and inherits all its functionalities right? Any guidance on this would be very much appreciated. Thank you so much.

[Fatima]

Hi! Is this the script that you use? If so, the def check part should be moved to the top.

Also if you're running check after reading the entire file, I think you should run it as you read each line (before sequence += line.strip()).

https://stackoverflow.com/questions/23657545/classes-with-exception

[Gonçalo]

Thank so much for your help. I will look at it carefully once I get back home after work :)

[Gonçalo]

That was very helpful thank you so much.

[cschu181]

Indeed, instead of the return False you'd raise BadSequenceException(x + " is not a valid nucleobase") (or something like that).

In addition to that, do you really want to add the empty sequence (upon encountering the first sequence header >) to the set of sequences?

[Gonçalo]

That makes sense and helped me a lot thank you very much :)