convert binary to charaacter

hello,

 i have a binary sequnce 10110001. and i want to encode based on the following rule
A=00
C=01
T=10
G=11
and the answer i get will be something like TGAC.
i want to do it for a 256*256 matrix each element having an 8bit binary sequence..i have generated the matrix by using the following code

>>a=imread('C:\Users\Abzz\Desktop\lena.png');

>>disp(a);

>>imshow(a);

>>for i=1:1:256

>>for j=1:1:256

>>b{i,j,1} = dec2bin(a(i,j),8);

>>end

>>end

>>disp(b)

pls help..thanks in advance

Answer 1

[Guillaume]

Personally, if I was going to do that encoding several times, I would precompute the encoding for all the possible values (there's only 256 of them) and use the precomputed array to do the conversion using basic matrix indexing. Thus the expensive calculation you only do once and the conversion from matrix to sequence is a simple array lookup, thus very fast.

You can precompute the array many different ways. A fairly simple one:

sequences = 'ACTG'; %in the order 0,1,2,3
seqbase4 = dec2base(0:255, 4); %convert integer 0-255 to a sequence of 0123
int2sequence = num2cell(sequences(seqbase4-'0'+1), 2); %represents integer 0-255 as cell array of ACTG

Whenever you want to convert a matrix, it's then as simple as:

a=imread('C:\Users\Abzz\Desktop\lena.png');
s=int2sequence(a+1); %+1 because matlab indexes start at 1

[Andrei Bobrov]

+1

Answer 2

[Azzi Abdelmalek]

str='10110001'
c='ACTG'
b={'00','01','10','11'}
ss=regexp(str,'.{2}','match')
[ii,jj]=ismember(ss,b)
out=c(jj)

%or

str='10110001'
c='ACTG'
out=c(bin2dec(regexp(str,'.{2}','match'))+1)

%or

str='10110001'
c='ACTG'
out=c(bin2dec(reshape(str,2,[])')+1)

[Abirami]

sir i understood the concept but i don't know how to apply it for the matrix..if i employ a loop im getting it wrong..pls help..

[Azzi Abdelmalek]

How is your matrix? give a short example

[Azzi Abdelmalek]

M={'10110001','10010010'} % Your matrix
str='10110001'
c='ACTG'
out=cellfun(@(x) c(bin2dec(reshape(x,2,[])')+1),M,'un',0)

[Abirami]

a={'00111011' '01110011' '11011101' '10110111'} sir this is just a sample. imagine a 256*256 matrix.

[Guillaume]

Did you matrix starts out as binary strings or as integer? If the latter, you don't need to convert to binary (which is the wrong base anyway, you're operating in base 4 not base 2)

[Abirami]

No sir initially the matrix is a decimal valued one which i convert to 8bit binary sequence..

[Guillaume]

Then see my answer. You have all the steps there.

[Abirami]

still not getting it sir..i'm new to Matlab so im not able to understand it easily..can u pls elaborate sir so that i correct my code...

[Guillaume]

Have you tried what I wrote in my answer? Does it not work for you? If it doesn't, which step is the problem?

[Azzi Abdelmalek]

a=imread('C:\Users\Abzz\Desktop\lena.png');
[n,m]=size(a);
b=arrayfun(@(x) dec2bin(x,8),a,'un',0);
c='ACTG';
out=cellfun(@(x) c(bin2dec(reshape(x,2,[])')+1),b,'un',0)

Note that Guillaume's method is faster, and do not need to convert your matrix from decimal to binary