A = [ 18 4; 15 12; 12 0; 6 44 ;8 3; 2 22; 3 67; 5 32; 20 32; 10 4];I have this matrix and i want to get the percentage of having numbers less than 10
MATLAB: Calculating the percentage of numbers in the matrix
matrixpercentage
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mlinverse_size = ((7824*7824)*8) *19 X_size = (85*7824)*8total_size = mlinverse_size + X_sizetotal_size_as_gigabytes = total_size / 1024 / 1024 / 1024mlinverse_size = 9304676352X_size = 5320320total_size = 9309996672total_size_as_gigabytes = 8.67061007022858Have you considered using spdiags() for your diagonal matrices?
[rnaFile, message] = fopen(outputFile, 'w');While not your problem, should check for the output file opening successfully as well as input...
[base, num] = fread(dnaFile, 1, 'char');The above reads one character, but returns it as a double, not a character.
Use
[base, num]=fread(dnaFile,'*char');to read whole file into a character array.
while num > 0 if base == 'C' ...The above starts an infinite loop as num=1 and there's nothing inside the loop that ever changes num so it stays there forever...oh, although it will eventually error out on EOF on the read...scanned too quickly first.
You can loop, but Matlab is vectorized; may as well make use of it.
% rewrite the rules for convenience C -> G; G -> C; T -> A; A -> U
out=repmat('_',size(base)); % this is else case...we'll overwrite everything besides
out(base=='C')='G'; % use logical addressing to locate each and write output
out(base=='G')='C';out(base=='T')='A';out(base=='A')='U';freqG=sum(out=='G');freqC=sum(out=='C');freqA=sum(out=='A');freqU=sum(out=='U');totalNum=sum([freqG freqC freqA freqU]);freqG=sum(out=='G')/totalNum;freqC=sum(out=='C')/totalNum;freqA=sum(out=='A')/totalNum;freqU=sum(out=='U')/totalNum;ADDENDUM:
Couldn't see an issue otomh so did a trial with just made up sequence...
>> dna=['A', 'C', 'G', 'T']; % the four letters start with
>> dna=repmat(dna,1,10); % make longer sequence from them
>> dna=dna(randperm(length(dna))); % and then scramble 'em up
>> dna(randperm(length(dna),3))='_'; % a few other characters for spice
>> dna % what we start with is then ...
dna =CTTGCCTCC_GGA_ATGAATGCAACACAGTT_GGTGCATCThe algorithm above starts here:
>> rna=repmat('_',size(base)); % replace the non-wanted letters
>> rna(dna=='C')='G';>> rna(dna=='G')='C';>> rna(dna=='T')='A';>> rna(dna=='A')='U';>> [dna;rna] % see what we got...
ans =CTTGCCTCC_GGA_ATGAATGCAACACAGTT_GGTGCATCGAACGGAGG_CCU_UACUUACGUUGUGUCAA_CCACGUAGLooks like what problem statement asked for...compute frequency
Did this in "more Matlab-y" way; order is alphabetic to satisfy histc
>> RNA='ACGU'; % the letters to use as bin centers must be increasing order
>> freq=histc(rna,RNA)freq = 9 9 10 9>> freq=freq/sum(freq)freq = 0.2432 0.2432 0.2703 0.2432>> >> [RNA.' num2str(freq.','%.4f')] % display results tabulated
ans =A 0.2432C 0.2432G 0.2703U 0.2432>>If order is important revert to previous or a "cute" way would be to use the categorical datatype--
>> rnac=categorical(cellstr(rna),{'G';'C';'A';'U';'_'});>> summary(rnac) G 10 C 9 A 9 U 9 _ 3 >>ADDENDUM 2:
And, the yet more Matlab-y way vectorizes the translation via lookup...
>> DNA=['C','G','T','A','_']; % base characters in sequence 1
>> RNA=['G','C','A','U','_']; % corresponding characters in sequence 2
>> RNA(arrayfun(@(c) find(c==DNA),dna)) % translate one to other...
ans =GAACGGAGG_CCU_UACUUACGUUGUGUCAA_CCACGUAG
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