extractBefore function not giving correct answer.

I have a protein sequence and I want to make fragments of it. for example the protein sequence is 'MSKAHFRQWTYVSKATYQRW' and the fragments should be 'M', 'MS', 'MSK', 'MSKA', 'MSKAH', 'MSKAHF', 'MSKAHFR', 'MSKAHFRQ' and so on. Im using the following code:

seq = 'MSKAHFRQWTYVSKATYQRW';

frag = [];

for i = 1:length(seq)

    ii = extractBefore (seq, seq(i));

frag = [frag char (length(seq)) ii];

end

frag

But after some loops it does not follow the rule and starts giving wrong answers. The output is :

'M MS MSK MSKA MSKAH MSKAHF MSKAHFR MSKAHFRQ MSKAHFRQW MSKAHFRQWT MSKAHFRQWTY M MS MSK MSKAHFRQW MSKAHFRQWT MSKAHFR MSKAHF MSKAHFRQ'

please help. TIA.

Answer 1

[Birdman]

The following code simply does what you want:

seq = 'MSKAHFRQWTYVSKATYQRW';
for i=1:numel(seq)
    Seq{i}=seq(1:i);
end

The outputs are stored in a cell array, you can see any fragment by typing

 Seq{1}
 Seq{2}

and so on.

[amna chaudhary]

Thanks a lot. God bless you abundantly. Was stuck on this for quite a long time now

Answer 2

[Steven Lord]

So at iteration n you want the first n characters from the text? If you're using a char vector, just use indexing.

word = 'hello';
for k = 1:length(word)
  fprintf('%s\n', word(1:k));
end

If you're using a string, use extractBetween.

word = "hello";
for k = 1:strlength(word)
  fprintf('%s\n', extractBetween(word, 1, k));
end

[amna chaudhary]

Thanks a lot. Super amazingg!