WIP. Porting bash pipeline script to python.

Added code to load environment modules from within a python script. Also general bugfixes and additional functionality. Still a work in progress, so is not yet complete.
Absolutely!
But again, is just a good practice, not that something is wrong.
There are a list of Built-in exceptions in python that modules use to say: "I've failed because of this". The list can be found [here](https://docs.python.org/2/library/exceptions.html). What I was saying is that, instead of printing a message, you can raise RuntimeError, or even better IOError with that message. This way the error will be more standard and the user will be able to see the traceback. That would be:
```python
for fname in input_fast_list:
    if not os.path.isfile(fname):
        raise IOError("Fatal error - can't find input file {}".format(fname))
```
This will terminate the program properly :-)