Make basic genome sequence program work properly

Question

I tried to create a program to check the genome sequence.

Context:

Biologists use a sequence of letters A, C, T and G to model a genome.
A gene is a substring of a genome that starts after a triplet ATG and ends before a triplet TAG, TAA, or TGA.
Furthermore, the length of a gene string is a multiple of 3 and the gene does not contain any of the triplets ATG, TAG, TAA and TGA.

My desired result is:

>>Enter a genome string:>>TTATGTTTTAAGGATGGGGCGTTAGTT
Output:
>>TTT
>>GGGCGT
>>Enter a genome string:>>TGTGTGTATAT
>>No gene is found

So far I have got:

import re

def findGene(gene):
  pattern = re.compile(r'ATG((?:[ACTG]{3})*?)(?:TAG|TAA|TGA)')
  return pattern.findall(gene)

  findGene('TTATGTTTTAAGGATGGGGCGTTAGTT')

def main():
  geneinput = input("Enter a genome string: ")
  print(findGene(geneinput))


main()

# TTATGTTTTAAGGATGGGGCGTTAGTT

How can I make this code work properly?

Thank you.

What are examples of input and output that suggest this is not working correctly? — jarmod, May 14 '20 at 13:54
Your code seems to work fine for me: https://repl.it/@HarunYlmaz/genome — Harun Yilmaz, May 14 '20 at 13:57
yes, it is working but when I try to get output for 'TGTGTGTATAT' the output is always '[]' instead of 'No gene is found.' I want the program to give 'No gene is found' output if the gene sequence is incorrect. — Raj, May 14 '20 at 14:12
One option: `print(findGene('TGTGTGTATAT') or 'No gene is found')` — jarmod, May 14 '20 at 14:38
@jarmod Thank you, I am able to find my desired code with your help. Thanks a lot. — Raj, May 14 '20 at 15:07

score 1 · Answer 1 · answered May 14 '20 at 15:05

1

import re

def findGene(gene):
    pattern = re.compile(r'ATG((?:[ACTG]{3})*?)(?:TAG|TAA|TGA)')
    return pattern.findall(gene)

findGene('TTATGTTTTAAGGATGGGGCGTTAGTT')

def main():
    geneinput = input("Enter a genome string: ")
    print(findGene(geneinput) or 'No gene is found')


main()

# TTATGTTTTAAGGATGGGGCGTTAGTT

answered May 14 '20 at 15:05

Raj

21
2

In case you need to be able to explain why this works, you need to understand the notion of 'truthy' and 'falsy' (sometimes spelled 'falsey'). See https://stackoverflow.com/questions/39983695/what-is-truthy-and-falsy-how-is-it-different-from-true-and-false – jarmod May 14 '20 at 15:18

Make basic genome sequence program work properly

Context:

My desired result is:

So far I have got:

1 Answers1