You can render your file and save its output with blender's default terminal options, or you can process data in the scene with a python script called from the terminal. For a general idea of how to use the terminal flags, see the wiki manual here:
For a full list of terminal flags, run
./blender --help from a terminal. Also see this answer for using a python script from the terminal:
How to enable an addon on startup via script?
What I am understanding is you want to render out image data, not animation data. If you are rendering out into a video file, I would recommend instead to render into an image sequence, which you can then compile into a video. You can easily do this through FFMPEG or the VSE. This is because if blender crashes during render, you don't need to splice together a number of video files; you can simply continue where you left off without worry.
If you want to export animation data for use in another program, you will have to export the animation through one of the exporters, not through rendering. If you're using the BGE, you don't need to export your animation data, as the BGE is integrated and has direct access to your scene. If you're using external software, like Maya or Unity, you will need to use the FBX or Collada exporters, which are included with blender.
If you could clarify what you're asking for, we can be more specific in our answers. As it is, it's somewhat ambiguous what you're asking for.