how can i count the number of times that the symbol appears?

seq1 = ["AQSVPWGISRVQAPAAHNRGLTGSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQDGN"+...
"GHGTHVAGTIAALNNSIGVLGVAPSAELYAVKVLGASGSGSVSSIAQGLEWAGNNGMHVA"+...
"NLSLGSPSPSATLEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGATDQNNNR"+...
"ASFSQYGAGLDIVAPGVNVQSTYPGSTYASLNGTSMATPHVAGAAALVKQKNPSWSNVQI"+...
"RNHLKNTATSLGSTNLYGSGLVNAEAATR"];
seq2 = ["MRQSLKVMVLSTVALLFMANPAAASEEKKEYLIVVEPEEVSAQSVEESYDVDVIHEFEEI"+...
"PVIHAELTKKELKKLKKDPNVKAIEKNAEVTISQTVPWGISFINTQQAHNRGIFGNGARV"+...
"AVLDTGIASHPDLRIAGGASFISSEPSYHDNNGHGTHVAGTIAALNNSIGVLGVAPSADL"+...
"YAVKVLDRNGSGSLASVAQGIEWAINNNMHIINMSLGSTSGSSTLELAVNRANNAGILLV"+...
"GAAGNTGRQGVNYPARYSGVMAVAAVDQNGQRASFSTYGPEIEISAPGVNVNSTYTGNRY"+...
"VSLSGTSMATPHVAGVAALVKSRYPSYTNNQIRQRINQTATYLGSPSLYGNGLVHAGRATQ"];

[Score_global, Alignment_global] = nwalign(seq1,seq2,ScoringMatrix="blosum62");


for i=1:361
    cont = 0;
    if Alignment_global(2,i) == '|' || ':'
        cont=cont+1;
    else
        cont=cont
    end
end

i have the alignment_global and i want to count how much times i have ":" and "|" in the second row.

i did a for loop that pass on the whole second row!!

but i get that cont=1!!!

why the loop didnt count all the times!!

can u help me?

Answer 1

[Voss]

One thing to do is not to reset the count to zero each time through the for loop. See modified code (including other modifications) below:

seq1 = ["AQSVPWGISRVQAPAAHNRGLTGSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQDGN"+...
"GHGTHVAGTIAALNNSIGVLGVAPSAELYAVKVLGASGSGSVSSIAQGLEWAGNNGMHVA"+...
"NLSLGSPSPSATLEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGATDQNNNR"+...
"ASFSQYGAGLDIVAPGVNVQSTYPGSTYASLNGTSMATPHVAGAAALVKQKNPSWSNVQI"+...
"RNHLKNTATSLGSTNLYGSGLVNAEAATR"];
seq2 = ["MRQSLKVMVLSTVALLFMANPAAASEEKKEYLIVVEPEEVSAQSVEESYDVDVIHEFEEI"+...
"PVIHAELTKKELKKLKKDPNVKAIEKNAEVTISQTVPWGISFINTQQAHNRGIFGNGARV"+...
"AVLDTGIASHPDLRIAGGASFISSEPSYHDNNGHGTHVAGTIAALNNSIGVLGVAPSADL"+...
"YAVKVLDRNGSGSLASVAQGIEWAINNNMHIINMSLGSTSGSSTLELAVNRANNAGILLV"+...
"GAAGNTGRQGVNYPARYSGVMAVAAVDQNGQRASFSTYGPEIEISAPGVNVNSTYTGNRY"+...
"VSLSGTSMATPHVAGVAALVKSRYPSYTNNQIRQRINQTATYLGSPSLYGNGLVHAGRATQ"];
[Score_global, Alignment_global] = nwalign(seq1,seq2,ScoringMatrix="blosum62");
cont = 0;
for i=1:361
    if Alignment_global(2,i) == '|' || Alignment_global(2,i) == ':'
        cont=cont+1;
    end
end
disp(cont);

   241

[Sarah Nasra]

thank u!!!

Answer 2

[Walter Roberson]

You initialize your counter in each iteration. After any one iteration the counter will be either 0 or 1, but either way the next iteration you reset to 0. At the end of the loop the counter reflects only the last test.

MATLAB does not offer a way to test for multiple values using the syntax

value == constant1 || constant2

MATLAB interprets that as

(value == constant1) || (constant2)

which is two completely different logical tests. In MATLAB the evaluation of a value or constant as a logical condition, without a relationship operator, is completely valid, and is equivalent to testing that the value is non-zero. The constant ':' is non-zero so your code is equivalent to

(value == constant1) || true

and no matter what the value test came out as, the overall result is going to be true

I suggest that you consider using ismember()

[Sarah Nasra]

thank u!!