Python 3 support: use general fixes and six for 2 and 3 support

[chapmanb]

Builds on top of miRTop/mirtop#50 to add Python 3 support for seqcluster, as a prelude to working on this in bcbio. This also uses six and generic changes where applicable and tests currently pass on both 2 and 3.

• Moves from progressbar (no 3 support) to progressbar2, which dependency and code changes
• Add six as a dependency and use for generally specifying basestring/str.
• Use six.next for general iteration where needed.
• Add NumpyEncoder to handle issues with dumping to json since it can't serialize numpy arrays or int64s.
• Avoid string/byte error when reading stdout from RNAfold.
• Avoid changes in iterators/lists from 2/3 by enumerating with list.
• Small changes that trigger lint errors on 3 (avoiding bare raise statements)

[chapmanb]

Lorena -- thanks again for the discussion and pointers to the devel work. Closing in favor of #38 which handles this against the latest code.