Python find function not working. What am I doing wrong?

Question

I'm a hobbyist programmer (my actual my actual major is biology), so I apologize if the code is atrocious.

Anyway, I'm doing a rosalind.info exercise (http://rosalind.info/problems/subs/) that wants to me find every index where a specific DNA motif is contained within a larger DNA sequence. Basically, I need to find the indexes of a substring in a string. Should be easy, right? Well, maybe you can help me.

So here's my code:

with open('rosalind_subs.txt') as f:
    seq = f.readline()
    seq.strip()
    subs = f.readline()
    subs.strip()
    break

def finder(x, y):
    index = x.find(y)
    return index

print("sequence is: " + seq)
print("subs is: " + subs)

print(finder(seq, subs))

And here's my output:

sequence is:  ACCAGTCTCTTTTTTCTCTTTTCTCTTTTCTCTTTTGACCCTCTTTTCGTCACTCTTTTACCTCTTTTTCTCTTTTACTCTTTTCTCTTTTACTCTTTTACTCTTTTAGCGCAGATCTCTTTTCTCTTTTGGCTCTTTTGTCATCCTCTTTTAGACTCTTTTGGGAAGCGACGCCTCTTTTCTCTTTTCTCTTTTGCCTCTTTTTATAACCTAAAAGACTCTTTTCCCTCTTTTCCGATTTGCCAAGGGCTCTCTTTTCTCTTTTGCTCTTTTCTCTTTTCTCTTTTTACTCTTTTCTCTTTTCGCCCCAAGATTAACTCTTTTTCTCTTTTCTCTCTTTTTTCCTCTTTTCTCTTTTGAATTGACCTCTTTTTCTCTTTTTTTGGGCCGCTCTTTTCTCTTTTACTCTTTTCTCTCTTTTAACAGCTCTTTTCCTTCTCTTTTGTCTCTTTTAGTATACTCTTTTACTCTTTTCTCTTTTCTCTCTTTTACTCTTTTGCTCTTTTCTCTTTTTGTCTCTTTTGCCCTGTCTCTTTTCACGCTTCTCTTTTAGTGTACTCTTTTACTCTTTTTGGCTCTTTTCGAATTTGTTAGCTCTTTTGCTCTTTTCTCTTTTGCTCTTTTGTCTCTTTTGATCAGATTCTCTTTTTCTCTTTTCTCTTTTCCTTAAGCAGATTTCTCTTTTCTCTTTTTCTCTCTTTTGCTCTTTTACTCTTTTACTGCTTTCTCTTTTACAACCTCTTTTACTCTTTTAAGCTCTTTTCTCTTTTGCGCCTCTTTTCCTCCCCTCTTTTTAGCTCTTTTCTCTTTTTCGCTCTTTTCAGCTCTTTTCACTCTTTTGTTTTGAGCTCTTTTCAGACTCTTTTATCCTCTTTTTTCCTCTTTTAGCGCTCTTTTGTAGCCTCTTTT

motif is: CTCTTTTCT

-1

***Repl Closed***

I left the ***Repl Closed*** in there in an effort to leave no stone unturned. Maybe it has something to do with Sublime REPL?

Anyway, you probably can't tell just by looking, but the motif is actually found MANY times in the DNA sequence, it's just the find function isn't picking up on it. What gives?

Answer 1

break is not applicable in with scope. Please remove and try it. I have tested below code.

with open('rosalind_subs.txt') as f:
    seq = f.readline()
    seq.strip()
    subs = f.readline()
    subs.strip()

def finder(x, y):
    index = x.find(y)
    return index

print("sequence is: " + seq)
print("subs is: " + subs)

print(finder(seq, subs))

The output is

>>> 
sequence is: ACCAGTCTCTTTTTTCTCTTTTCTCTTTTCTCTTTTGACCCTCTTTTCGTCACTCTTTTACCTCTTTTTCTCTTTTACTCTTTTCTCTTTTACTCTTTTACTCTTTTAGCGCAGATCTCTTTTCTCTTTTGGCTCTTTTGTCATCCTCTTTTAGACTCTTTTGGGAAGCGACGCCTCTTTTCTCTTTTCTCTTTTGCCTCTTTTTATAACCTAAAAGACTCTTTTCCCTCTTTTCCGATTTGCCAAGGGCTCTCTTTTCTCTTTTGCTCTTTTCTCTTTTCTCTTTTTACTCTTTTCTCTTTTCGCCCCAAGATTAACTCTTTTTCTCTTTTCTCTCTTTTTTCCTCTTTTCTCTTTTGAATTGACCTCTTTTTCTCTTTTTTTGGGCCGCTCTTTTCTCTTTTACTCTTTTCTCTCTTTTAACAGCTCTTTTCCTTCTCTTTTGTCTCTTTTAGTATACTCTTTTACTCTTTTCTCTTTTCTCTCTTTTACTCTTTTGCTCTTTTCTCTTTTTGTCTCTTTTGCCCTGTCTCTTTTCACGCTTCTCTTTTAGTGTACTCTTTTACTCTTTTTGGCTCTTTTCGAATTTGTTAGCTCTTTTGCTCTTTTCTCTTTTGCTCTTTTGTCTCTTTTGATCAGATTCTCTTTTTCTCTTTTCTCTTTTCCTTAAGCAGATTTCTCTTTTCTCTTTTTCTCTCTTTTGCTCTTTTACTCTTTTACTGCTTTCTCTTTTACAACCTCTTTTACTCTTTTAAGCTCTTTTCTCTTTTGCGCCTCTTTTCCTCCCCTCTTTTTAGCTCTTTTCTCTTTTTCGCTCTTTTCAGCTCTTTTCACTCTTTTGTTTTGAGCTCTTTTCAGACTCTTTTATCCTCTTTTTTCCTCTTTTAGCGCTCTTTTGTAGCCTCTTTT

subs is: CTCTTTTCT
15

Answer 2

Also a fellow biologist here who has done several rosalind.info exercises.

First of, your code to read in the sequence and the motif could be improved by using splitlines(), which takes care of removing the newline. also notice how I use tuple unpacking to assign both the seqand motif variable at once.

with open('rosalind_subs.txt') as f:
    seq, motif = f.read().splitlines()

Next, you correctly noticed that find only returns the index of the first occurrence of your motif. To find all the occurrences, it helps to know that find takes another optional argument start. If you provide that, it starts to look from that index position. Use this in a loop and you get all your indexes.

Another approach is to use regular expressions. Beware that motifs can overlap each other, so you need to make use of a lookahead assertion.