Abstracting out File IO

[mortonjt]

Looking over all of the bfillings commands, most of the inputs and outputs are filepaths. This is a bit cumbersome, since it is requiring the user specify every input and output filepath if they wanted access the python API.

I think it would be much more preferable to abstract out the file IO and pass around iterators of Sequence objects. This would ultimately save time and trouble bookkeeping.

If we go down this route, we'd need to consider where will temporary files be stored/created. This would definitely be useful to have around for debugging purposes.