Iterate string to compare an i element to i+1 element python

Question

I have a DNA sequence:

seq='AACGTTCAA'

I want to count how many letters are equal to the next one. In this example I should get 3 (because of AA-TT-AA).

In my first try I found out that this doesn't work, because i is a string and 1 an integer.

seq='AACGTTCAA'
count=[]
for i in seq:
    if i == i+1: #neither i+=1
        count.append(True)
    else: count.append(False)
print(sum(count))

So I tried this:

seq='AACGTTCAA'
count=[]
for i in seq:
    if i == seq[seq.index(i)+1]:
        count.append(True)
    else: count.append(False)
print(sum(count))

Then I receive this output which I cannot understand. 3 of these True should be False (1,5,8) Especially 8 as it is the last element of the string.

6
[True, True, False, False, True, True, False, True, True]

If thought about doing this with arrays but I think there might be a easy way to do this just in strings. Thanks

I think your index call always returns the first location of the character you're looking for, so that's why you're seeing too many `True`s ( [doc](https://docs.python.org/3/library/stdtypes.html#str.index) ) . I would do it as suggested in the answer by @bichanna below — Heath, Dec 08 '21 at 15:42

score 2 · Accepted Answer · answered Dec 08 '21 at 15:55

To answer your question, the statement for i in seq yields a series of string variables like 'A', 'A', 'C' etc. so when in your first case when you are attempt to compare i == i+1: you are adding 1 to a string variable which throw a TypeError. In your second example, where you execute if i == seq[seq.index(i)+1] gives a false result, since the seq.index(i) always returns the first occurrence of the value. To do what you want on a basic level you can do the following:

def countPairedLetters(seq):
    count = 0
    for i in range(1, len(seq)):
        # i starts with 1 and ends with len(seq)-1
        if seq[i-1] == seq[i]:
            count += 1
    return count

Note: by starting with the index 1 and going to last, you avoid the issue with overrunning the sequence.

score 1 · Answer 2 · 2021-12-08T16:19:51.443

1

You can do this:

for i in range(0, len(seq)):
   if seq[i] == seq[i+1]: # <- this causes an error
      count.append(True)

Though you have to check if seq[i+1] does not cause an error.

Update

count = 0
for i in range(0, len(seq)-1): # this prevents an error
   if seq[i] == seq[i+1]:
      count += 1

edited Dec 08 '21 at 16:19

answered Dec 08 '21 at 15:37

The loop should run to `len(seq) - 1` to avoid overrun. Your current implementation will raise an error – Mad Physicist Dec 08 '21 at 15:58
Yes, that's right. I said so in the answer. – Dec 08 '21 at 15:58
Also, keeping the count in a list won't help you get the count. – Mad Physicist Dec 08 '21 at 15:58
It's what the OP is doing. I just copied. – Dec 08 '21 at 15:59
Instead of saying it, you should post code that isn't broken. If OP is doing the wrong thing, the whole point of answering is to correct them. – Mad Physicist Dec 08 '21 at 15:59
Okay. I'll update. – Dec 08 '21 at 16:01
Please remove the broken code. It's better to add a line of prose explaining what you fixed. Thanks for understanding. – Mad Physicist Dec 08 '21 at 16:18

vaizki · Answer 3 · 2021-12-08T16:05:21.667

1

Using itertools is one way:

from itertools import groupby
seq = 'AACGTTCAA'
print(sum(len(list(g))-1 for k,g in groupby(seq)))

This splits the sequence into groups of consecutive letters, then counts each group's lenght-1 into the total.

Edit: Updated with mozway's comments.

edited Dec 08 '21 at 16:05

answered Dec 08 '21 at 15:46

vaizki

1,678
1
9
12

2

This won't work (AAAA would count as 1 instead of 3), you have to sum the len-1 – mozway Dec 08 '21 at 15:49
You are correct, I did not realize this case from the example sequence. Updated the answer. It is not so pretty anymore but still a decent oneliner. – vaizki Dec 08 '21 at 15:53
You just had to replace `>1` by `-1`, groups of 1 item would yield 0 ;) – mozway Dec 08 '21 at 16:00
Yes that's prettier although might be even more confusing to some. Let's do it :) – vaizki Dec 08 '21 at 16:02
I don't think it's confusing, one just need to know how `groupby` works – mozway Dec 08 '21 at 16:04
Now it's beautiful ;) – mozway Dec 08 '21 at 16:05

score 0 · Answer 4 · answered Dec 08 '21 at 15:50

The reason for unwanted True's is because of seq.index()

index(), would always return the first occurrence of the character you are searching for. When you have 2 consecutive characters, its actually returning the index of the first occurrence of that character and they always match.

here is a quick solution:

seq='AACGTTCAA'
count=[]
for i in range(0,len(seq)-1):
    print(i)
    if seq[i]==seq[i+1]:
        count.append(True)
    else: count.append(False)
print(count)

Iterate string to compare an i element to i+1 element python

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