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Loop not working to find min,max,mean

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Marios Christofides
Marios Christofides on 12 Jul 2020 at 23:27
Commented: Geoff Hayes on 13 Jul 2020 at 11:46
I am running a for loop to determine the min,max, and mean of a DNA sequence. When I try to run the program it outputs zero as the value of the min max and mean. I can't find a solution to why the loop is not running properly. Does anyone have a fix?
load('chr1_sect.mat')
numBases = length(dna);
startPoint = 0; nump = 0;
for k = 1:3:numBases-2
if startPoint == 0
if dna(k) == '1' && dna(k+1) == '4' && dna(k+2) == '3'
startpoint = k;
end
else
if ((dna(k)) == '4' && dna(k+1) == '1' && dna(k+2)) == '1' ||...
(((dna(k))) == '4' && dna(k+1) == '1' && dna(k+2)) == '3' ||...
(((dna(k))) == '4' && dna(k+1) == '3' && dna(k+2)) == '1'
nump = nump +1;
SavedPoints(np,1) = startPoint;
SavedPoints(np,2) = k;
startPoint = 0;
end
end
end
x = min(nump)
y = max(nump)
z = mean(nump)

  1 Comment

Stephen Cobeldick
Stephen Cobeldick on 13 Jul 2020 at 4:22
Note that you can probably replace those repeated logical operations e.g.:
dna(k) == '1' && dna(k+1) == '4' && dna(k+2) == '3'
with simpler
strcmp(dna(k:k+2),'143')
or
isequal(dna(k:k+2),'143')

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Accepted Answer

Geoff Hayes
Geoff Hayes on 13 Jul 2020 at 1:50
Marios - from your code
nump = nump +1;
will always be a scalar (1x1) value which seems incorrect. Should this be an array of values? As for why, nump is always zero
if startPoint == 0
if dna(k) == '1' && dna(k+1) == '4' && dna(k+2) == '3'
startpoint = k;
end
else
note how the condition is for startPoint == 0 but you then initialize startpoint = k....which is a different variable because of the lower-case p. Try changing this to
if startPoint == 0
if dna(k) == '1' && dna(k+1) == '4' && dna(k+2) == '3'
startPoint = k; % <---- note the difference
end
else
and see what happens.

  2 Comments

Marios Christofides
Marios Christofides on 13 Jul 2020 at 1:55
Thank you. How should I change nump to be a vector while still being updated?
Geoff Hayes
Geoff Hayes on 13 Jul 2020 at 11:46
Marios - what are you trying to save on each iteration of the loop?

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