don't use sys.exit in fucntions

[jkoelker]

sys.exit() should only be called sparingly and usually not with 0.

Functions that need to report a non-zero status, should raise exceptions. The main function should catch these exceptions and translate them into an exit code which main would return.

Then in the if name == 'main' portion it would change to :
exit = main()
if exit:
sys.exit(exit)

[neogenix]

Removed sys.exit(0) with #27.

Still need to refactor 'main' section.