Best way to call terminal command again

I am using mencoder

to split files and I would like to turn this into an object oriented approach if possible using Java or similar for example. But I'm not sure if this is the best way, so I leave it open. This is what I need:

I have an excel file with a start time and end time and I need to extract the corresponding clips from a video file. In terminal (I am on Mac OS X) I had success, for example:

mencoder -ss 0 -endpos 10 MyVideo.avi -oac copy -ovc copy -o Output.avi

      

        
        
        
      

    

Which creates the Output.avi video by clipping the first 10 seconds of the MyVideo.avi video.

But as I said, I want to make the program read the excel file and call this mencoder command multiple times (over 100) for each start and end time.

I know how to read in an excel file in Java, but I'm not sure what is the best way to call this command from Java. Also, I would like to see the output mencoder

(because it prints a good percentage, so you know how long one command will take). Can this be done in a shell script? I would like to really

use Java if possible as I have years of experience in Java and no experience in shell scripting.

UPDATE

Here is what I tried in Java but it freezes when in.readLine()

        File wd = new File("/bin");
        System.out.println(wd);
        Process proc = null;
        try {
           proc = Runtime.getRuntime().exec("/bin/bash", null, wd);
        }
        catch (IOException e) {
           e.printStackTrace();
        }
        if (proc != null) {
           BufferedReader in = new BufferedReader(new InputStreamReader(proc.getInputStream()));
           PrintWriter out = new PrintWriter(new BufferedWriter(new OutputStreamWriter(proc.getOutputStream())), true);
           out.println("cd ..");
           out.println("pwd");
           String video = "/Users/MyFolder/MyFile.avi";
           String output = "/Users/MyFolder/output.avi";
           int start = 0;
           int end = 6;
           String cmd = "mencoder -ss " + start + 
                          " -endpos " + end + 
                          " " + video + " -oac copy -ovc copy -o " + output;

           out.println(cmd);
           try {
              String line;
              System.out.println("top");
              while ((line = in.readLine()) != null) {

                 System.out.println(line);
              }
              System.out.println("end");
              proc.waitFor();
              in.close();
              out.close();
              proc.destroy();
           }
           catch (Exception e) {
              e.printStackTrace();
           }
        }