Replacing characters with integers in a very long string

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Paolo Binetti 2016-12-17

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评论： Star Strider 2016-12-18

I have a string of a few millions characters, want to replace it with a vector of integers according to simple rules, such as 'C' = -1 and so forth. My implementation works but takes forever and uses gigabytes of memory, in particular due to the str2num function, to my understanding. Is there a way to go more efficiently?

sequence = fileread('sourcefile.txt');
sequence_num =  strrep(sequence,    'A', '0 '); 
sequence_num =  strrep(sequence_num,'C','-1 ');
sequence_num =  strrep(sequence_num,'G', '1 ');
sequence_num =  strrep(sequence_num,'T', '0 ');
sequence_num =  regexprep(sequence_num,'\r\n','');
sequence_num = str2num(sequence_num);
sequence_num = int32(sequence_num);

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采纳的回答

Star Strider 2016-12-17

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I don’t know what structure ‘sequence’ has. I created it as a cell array here:

bases = {'A','C','T','G'};                          % Cell Array
sequence = bases(randi(4, 1, 20));                  % Create Data
skew = zeros(1, length(sequence)+1,'int32');        % Preallocate
Cix = find(ismember(sequence, 'C'));                % Logical Vector
Gix = find(ismember(sequence, 'G'));                % Logical Vector
skew(Cix+1) = -1;                                   % Replace With Integer
skew(Gix+1) = +1;                                   % Replace With Integer

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Paolo Binetti 2016-12-18

Thank you @Star and @Jan. All in your help sped up my code 700x times, now 0.17 s for a bacterium genome. About 250 times thanks to @Star suggestions, and 3 more times thanks to @Jan final simplification.