Write functions counting the DNA sequence of codon " ATG "

Question

the content of my tasks are "Write functions counting the DNA sequence of codon " ATG "

I did something like that but I do not know what is wrong with that

def seq(dna):
    dna = dna.count("ATG")

print seq("ATGSDSGFAGEFRASFWET")

Please help me

You did not indent the function body. Otherwise, you should state as specificly as posslible what you expect to happen, and what happens instead. — MB-F, Jan 13 '16 at 14:46
What is “counting the DNA sequence of codon ‘ATG’” supposed to mean? Count the frequency of the sequence? If so, then you cannot simply use the `count` method, it will give you wrong results because it will count frame-shifted “ATG” (e.g. “CATGTA” would return `1`, even though there’s no in-frame “ATG”). — Konrad Rudolph, Jan 13 '16 at 14:47
Use `return dna.count("ATG")` inside your function to return a value — Finwood, Jan 13 '16 at 14:49
I've written many of these before... you could use a modulo to make sure your sequence is divisible by three and returns codons or amino acids as well in your function. It's more of a sanity check. — Sean, Jan 13 '16 at 15:03

score 1 · Answer 1 · answered Jan 13 '16 at 14:52

1

1 - Strip your major string in a array of strings with size 3.

2 - Do an iteration in your array of strings and compare with string "ATG" - If the comparison is true, increment in 1 an int auxiliar variable

3 - Display the result of the auxiliar int variable

answered Jan 13 '16 at 14:52

Victor Viola

1

That's not gonna work: it is possible that `ATG` starts halfway the first substring: like `CAT GAT`. Furthermore it is inefficient. You can use the *Knuth-Moris-Pratt* algorithm to do this in one linear search. – Willem Van Onsem Jan 13 '16 at 14:53
1

of course it is gonna work. There is no sequence of proteins in DNA with less or more than 3 letters. – Victor Viola Jan 13 '16 at 14:56
I mean nucleoside triphosphate instead of proteins – Victor Viola Jan 13 '16 at 15:05
yeah I know that. But who says you have *the start of the DNA string*. You do not have to do all this expensive splitting, etc. – Willem Van Onsem Jan 13 '16 at 15:12
Who said the opposite? He is clearly a begginner, does not make sense to explain Knuth-Moris-Pratt approach or something similar. Just solving his problem at the moment. In the right moment he will face more complex questions. – Victor Viola Jan 13 '16 at 15:15

score 0 · Answer 2 · answered Jan 13 '16 at 14:52

0

i'm guessing you forgot to add return?

def seq(dna):
    dna = dna.count("ATG")
    return dna

print seq("ATGSDSGFAGEFRASFWET")

answered Jan 13 '16 at 14:52

Bear

2 Answers2