MATLAB string manipulation

string cell array

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ar = {'aa';'bbbbb'}

mat2str   (convert number to string)

======================

parameter = '-s 0 -t 0 -c ';

for c=1:2

    nextp = [parameter mat2str(  c) ]

end

string comparison

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 sa='ab';

 sb='aba';

 t = strcmp(sa , sb )

if( t == 1)

  display('Yest match');

else

   display('No match')

end

strmatch  find exact string in cell array

=======================

list = {'max', 'minimax', 'maximum', 'max'}

x = strmatch('max',list,'exact')

find  string starts with in cell array

=======================

list = {'max', 'minimax', 'maximum', 'max'}

x = strmatch('max',list)

String Comparison

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 strmatch('ab' , 'abc') ; % return 1

strcmp('ab' , 'abc') ; % return0

Find index of  char/ string strfind  find the pattern

====================

S = 'Find the starting indices of the pattern string';
strfind(S, 'in')
ans =
     2    15    19    45

Sub String

===================

s = s(1 : n) 

String trim

==========
out = strtrim(ins)

Reading from file  % parse each line

===========================

function createLogo

motifCount=0;

fNamePPM = '../gene.features.v2/v2_C_287_NC_48_profile.model'; % columns as Letter

fid = fopen(fNamePPM);

tline = fgets(fid);

while ischar(tline)

      if tline(1) =='*' % start of a motif    

           motifCount = motifCount + 1;

       

           tline = fgets(fid); % read ID

           %% tokenize the line

           remain  = tline;

           countToken = 0;

           while true

                [word, remain] = strtok(remain);

                if isempty( word  )

                    break;

                end

                countToken = countToken +1;

                if countToken ==2

                   motifLen = str2num(word);

                   profileMatrix = zeros(4,motifLen);

                end

            disp( word  );

           end

        tline = fgets(fid); % score

        tline = fgets(fid); % A

        profileMatrix(1,1:motifLen) = str2num(tline);

     end

     tline = fgets(fid); % to read for next iteration

   

end

fclose(fid);

end

String tokenizer ( strtok )

==============

remain  = wholeString;

    while true

       [word, remain] = strtok(remain);

       if isempty( word  ),  break;  end

       disp( word  );  

    end

% convert tab delimited line into vector of  number

=====================================

myvector = str2num( myLine );

Read file with FIXED COLUMN like matrix but content may be string

fid = fopen('scan1.dat');
C = textscan(fid, '%d\t%f\t%f\t%f\t%f'); % each row have 5 column
C{1} (1) ; % first column , 1st row
C{1} (2) ; % first column , 2nd row
fclose(fid);

[ covTarget covBG score source consensus ] = textread(fnameStat,'%f\t%f\t%f\t%s\t%s');

% here in the file there are 5 columns , first 3 are numeric, and last 2 are string

Write cell Array dlmwrite is not for cell array 

fid = fopen('LLGencodeCommonID.txt', 'w');
fprintf(fid, '%s\n', commonID{2}); % write 2nd column
fclose(fid);

sscanf:  Parsing word inside of a string

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     consensusSeq = fgetl(fid) % Consessus: AAACC

     curSeq = sscanf(consensusSeq,'%*s %s', [1, inf]) % curSeq = AAACC