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

[chapmanb]

This makes the code base compatible with Python 3 in a first step towards moving bcbio and dependencies. It uses six and general changes to make it both 2 and 3 compatible and tests pass for me on both. The changes are:

• Add six as a dependency.
• Use six for generally specifying basestring/str.
• Avoid changes in iterators/lists from 2/3 by enumerating with list.
• A few cleaned print statements

[codecov[bot]]

Codecov Report

Merging #50 into master will increase coverage by 0.01%. The diff coverage is 86.66%.

@@            Coverage Diff             @@
##           master      #50      +/-   ##
==========================================
+ Coverage   76.59%   76.61%   +0.01%     
==========================================
  Files          24       24              
  Lines        2064     2065       +1     
==========================================
+ Hits         1581     1582       +1     
  Misses        483      483

Impacted Files	Coverage Δ
mirtop/gff/merge.py	37.77% <0%> (ø)	:arrow_up:
mirtop/gff/validator.py	87.83% <100%> (ø)	:arrow_up:
mirtop/gff/convert.py	89.88% <100%> (ø)	:arrow_up:
mirtop/mirna/realign.py	91.15% <100%> (ø)	:arrow_up:
mirtop/importer/srnabench.py	82.31% <100%> (ø)	:arrow_up:
mirtop/gff/stats.py	72.97% <100%> (ø)	:arrow_up:
mirtop/gff/body.py	87.5% <100%> (ø)	:arrow_up:
mirtop/libs/do.py	61.01% <75%> (+0.67%)	:arrow_up:

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[chapmanb]

Lorena, thank you for the pointer to the dev branch work. Closing in favor of #51 which is based on that branch.