Merge in Jessica's additions

cc @wutron 

Let's use this pull request to coordinate merging in your updates.  We may even break this into separate smaller PRs.  I think main thing is that I now enforce code quality using pep8 and pyflakes. See [test_codequality](https://github.com/mdrasmus/compbio/blob/master/test/test_codequality.py). I am also using unit tests (`make test`) to prevent regressions, so we can use that to make sure your changes are good. I'll make a first pass on this.

Jessica's repo: https://github.com/wutron/compbio
Jessica's branch: https://github.com/wutron/compbio/tree/yjw