Python 3 compatibility

[AliciaSchep]

Based on #95 but with a few small fixes, updated setup.py, and an added test case.

[liz-is]

FWIW, I tried the py3 branch out on my data and it seems to work well. I didn't run the python 2 version to compare though.

The only thing I had to change was to add an extra import statement in bin/nucleoatac:

from multiprocessing import freeze_support