There are two options for sending output from MATLAB to the stdin of another program:
Use a combination of MATLAB and your system's command line to accomplish your desired workflow.
1. Generate the input for the external program in MATLAB and write it to a file:
>> f = fopen('programInput.txt');
>> fwrite(f, '...');
2. Use the '!' operator (or the 'system' command) to run a shell command to read the file, pipe the file contents to the programs stdin, and write the program stdout to a file.
>> !type programInput.txt | myprogram > output.txt
>> !cat programInput.txt | myprogram > output.txt
If you need to process the output of the program in MATLAB you can read the 'output.txt' file into MATLAB.
Use MATLAB support for Python or Java
MATLAB provides support for calling Python and Java libraries from within MATLAB. It is possible to start a process using Python or Java and manipulate the stdin / stdout of the process within MATLAB. Refer to the documentation for Java's ProcessBuilder or Python's subprocess.Popen.
For more information about MATLAB support for Python, refer to the following links:
For more information about MATLAB support for Java, refer to the following links: