How can I create a for loop to count the number of letters in my array?

I have the following array:

bases = [ t t g c g c a t g c g c a c a ]

I want to create a for loop that loops through the array and counts the number of g’s within it.

do i use the if function?

Answer 1

[madhan ravi]

Stephen's way is efficient but if you insist loop then:

bases = 't t g c g c a t g c g c a c a'
ctr=0;
for i = 1:numel(bases)
    if bases(i)=='g'
        ctr=ctr+1;
    end
end
number_of_gs=ctr

[Fope Ayo]

thank you!

[madhan ravi]

Anytime :)

[Fope Ayo]

if i want to count a different letter, can i do this with a while loop from the for loop?

[madhan ravi]

EDITED

bases = 't t g c g c a t g c g c a c a'
ctr=0;
ctr1=0;
i=1;
for i=1:numel(bases)
    if bases(i)=='t' 
        ctr=ctr+1;
    elseif bases(i)=='g'
       ctr1=ctr1+1;
    end
end
number_of_ts=ctr
number_of_gs=ctr1

[Fope Ayo]

one more question sorry!

i want to include the count for 2 letters in one for loop? how can i do so?

[Fope Ayo]

could you put this in a for format if possible?

[Fope Ayo]

it doesnt seem to provide the correct answer when run?

[Fope Ayo]

thanks very much for your help madhan

[madhan ravi]

You are welcome :)

[Fope Ayo]

is there a way i can use that for loop to calculate the ratio of G-C’s rather than g-t’s?

[madhan ravi]

you can use the same way for those

[Fope Ayo]

ive replaced the if primer with

if primer(i)==‘gc’

and this hasnt resulted in the answer of 5?

[madhan ravi]

Not clear what's primer and what why should it be 5 explain clearly

[Stephen23]

@Fope Ayo: note that primer(i) refers to one element of primer (i.e. one character), so you are testing if two different characters (i.e. g and c) are both equal to the same character. Clearly this will never be true.

Note that my answer already shows you how to count how many times a specific substirng occurs.

[Fope Ayo]

@madhan ravi sorry i meant bases

Basically I am trying to use the for loop created which counts the number of two elements e.g g’s and c’s, then use this for loop to calculate the GC ratio for the sequence

[Stephen23]

"Basically I am trying to use the for loop created which counts the number of two elements e.g g’s and c’s, then use this for loop to calculate the GC ratio for the sequence"

So is your aim to play around with loops, or is your aim to get answers from your code?

Answer 2

[Stephen23]

The simple MATLAB solution:

>> V = 'ttgcgcatgcgcaca';
>> nnz(V=='g')
ans =  4

Or to count occurances of all of the different letters:

>> U = unique(V)
U = 'acgt'
>> histc(V,U)
ans =
   3   5   4   3

I.e. 'a' occurs three times, 'c' occurs five times, 'g' occurs four times, and 't' occurs three times.

To count how many times a specific substring occurs:

>> numel(strfind(V,'gc'))
ans =  4

I.e. the substring 'gc' occurs four times.

[Fope Ayo]

thanks for this but i need to relate it to my for loop

[Stephen23]

"thanks for this but i need to relate it to my for loop"

This is MATLAB, so why bother using a for loop?

":...then use this for loop to calculate the GC ratio for the sequence"

You are wasting your time using loops:

>> V = 'ttgcgcatgcgcaca';
>> nnz(V=='g') / nnz(V=='c')
ans =  0.80000

[Fope Ayo]

i know this is matlab.

I’m using the for loop that madhan created.

It’s what I need for my subscript, I don’t belive i’m wasting my time but thanks for you help

[Fope Ayo]

Thanks for your input Stephen.

[Fope Ayo]

why are you deleting and editing your comments Stephen?

[Stephen23]

I often edit my comments for clarity and spelling. Some comments and answers that turn out to be superfluous to the discussion I will also remove.

I notice that you have opened a new question on this topic here:

https://www.mathworks.com/matlabcentral/answers/430982-i-require-a-function-to-find-a-strand-of-characters-within-a-matrix

which is clearer describing what you are actually trying to achieve. You should put a link back to this thread, so that readers of that new thread know what you have already tried and what information you have been given. Otherwise people often just give you the same solutions, which is unsatisfying for everyone involved.

[Fope Ayo]

Once again, thanks for your insight and input.