How to save text files to a different folder than read?

I have a lot of files that I need to process of the form "abcdef - ###.txt" where ### can be anywhere from 4 to 9 sequence of random numbers. I have some code that is reading each file using dlmread in a for loop. Each file will get modified in some way and eventually will be left with multiple matrices that I want to output each to a new .txt file in a separate folder from where I'm getting the data from that looks like "abcdef - ###_x.txt", "abcdef - ###_x.txt" etc... where x is 1:number of matrices extracted

I was able to use sprintf('%s_%d,filename,x) to get dynamic variable naming for the matrices but I can't figure out how to write (dlmwrite is what I tried) each matrix to a new file dynamically.

myDirectory = uigetdir;  %open directory

myFiles = dir(fullfile(myDirectory,'*.txt'));  %get files in folder

for k = 1:length(myFiles) %loop through each file in myFiles

      baseFileName = myFiles(k).name;

      filename = fullfile(myDirectory, baseFileName); 

      fprintf(1, 'Now reading %s\n', filename);

      data=dlmread(filename,'',1,0); %build data matrix from file

      filename=filename(1:end-4); %remove .txt from filename string

      [rows,cols] = size(data); %

      data_ext = data(:,[1,2,4]); %Extract time, flowrate (AU), concentration (AU)

      numInjections = 0; 

      prevInjecting = false;

      injectionData = []; %Empty injection array

      for i=1:rows %index from 1 to #rows

          currentFlow = data_ext(i,2); %flow at index i

          if currentFlow > 5 && ~prevInjecting %is flow @ i > 5 and not previously?
              numInjections = numInjections+1; %increase injection count
              prevInjecting = true; %injection status: ON
              injectionData(1,:) = data_ext(i,:); %%begin building array
          elseif currentFlow > 5 && prevInjecting %if not beginning of injection
              injectionData = [injectionData;data_ext(i,:)]; %%amend injection array with rows
          elseif currentFlow <= 5 && prevInjecting %end of injection
  %         
              injectionData(:,2)=injectionData(:,2).*(0.1/1024); %convert from AU to L/min
              injectionData(:,3)=injectionData(:,3).*0.005-.1584; %convert from AU to g/L

          %take this array and count with # of injections
              filename_inj = sprintf('%s_%d.txt',filename,numInjections);

              %dlmwrite(filename_inj,injectionData,'delimiter','\t');% write data to .txt file

              injectionData = []; %reset injection data array,
              prevInjecting = false; %injection status: OFF

          else
              prevInjecting = false; %injection status: OFF
          end
      end

end

[Michal Dobai]

I'm not sure, if I understand your question correctly. So right now your program is working as expected, but all files are being saved to MATLAB current folder instead of some different - user selected - folder, right?

If that's true, you have to get the path to output directory. At the beginning of your script you can add:

%select output directory
myOutputDirectory = uigetdir([],'Now select output directory')

And then you can build full path of output file using fullfile:

dlmwrite(fullfile(myOutputDirectory, filename_inj),injectionData,'delimiter','\t');