Fix pylint warnings

Resolves a number of discrete pylint warnings throughout the code base.

Demonstrable improvement anticipated in both ```make pylint``` output and thus also at khmer's [landscape.io](https://landscape.io/github/ged-lab/khmer/).

- [x] Is it mergable
- [x] Did it pass the tests?
- [x] If it introduces new functionality in scripts/ is it tested?
  Check for code coverage.
- [x] Is it well formatted? Look at `pep8`/`pylint`, `cppcheck`, and
  `make doc` output. Use `autopep8` and `astyle -A10 --max-code-length=80`
  if needed.
- [ ] Is it documented in the Changelog?
- [x] Was spellcheck run on the source code and documentation after changes
  were made?