Fix failing splicing compute tests and get rid of various code smells

[olgabot]

Because of the pandas update, some of the subsetting of dataframes got broken. This PR also removes a lot of commented out code that has been hanging around and shouldn't be

• Is it mergable?
• Did it pass the tests?
• If it introduces new functionality in is it tested?
  Check for code coverage. To run code coverage on only the file you changed,
  for example flotilla/compute/splicing.py, use this command:
  coverage run --source flotilla --omit=test --module py.test flotilla/test/compute/test_splicing.py
  which will show you which lines aren't covered by the tests.
• Do the new functions have descriptive
  numpydoc
  style docstrings?
• If it adds a new feature, is it documented as an IPython Notebook in
  examples/, and is that notebook added to doc/tutorial.rst?
• If it adds a new plot, is it documented in the gallery, as a .py file
  in examples/?
• Is it well formatted? Look at the output of make lint.
• Is it documented in the doc/releases/?
• Was a spellchecker run on the source code and documentation after
  changes were made?