Add prototype script to identify emerging clades

[trvrb]

Adds a command line script that fetches an existing Nextstrain build's tree and frequencies JSONs and tries to find emerging subclades within currently annotated clades.

[codecov]

Codecov Report

Merging #653 (e8620d1) into master (e209103) will increase coverage by 0.78%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #653      +/-   ##
==========================================
+ Coverage   28.59%   29.37%   +0.78%     
==========================================
  Files          39       39              
  Lines        5355     5703     +348     
  Branches     1314     1488     +174     
==========================================
+ Hits         1531     1675     +144     
- Misses       3768     3943     +175     
- Partials       56       85      +29     

Impacted Files	Coverage Δ
augur/tree.py	8.42% <0.00%> (-1.22%)	⬇️
augur/utils.py	37.33% <0.00%> (+3.14%)	⬆️
augur/filter.py	49.30% <0.00%> (+4.50%)	⬆️

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[trvrb]

@huddlej ---

Thanks so much for putting this script together. I was just spending more time working with clades and this is invaluable. I don't have any changes to request and I think I can merge this given that it's a single file in scripts/ and doesn't risk breaking anything.

Although, I don't understand how Codecov is reporting that this changes test coverage in tree.py, utils.py, filter.py. None of these files were touched by this PR. This seems very strange to me. Oh, is it that this isn't a true diff? Instead it's running tests on current master and running tests on this branch and seeing there's a difference? A little annoying, but perhaps not so much of an issue for more recent PRs.

[huddlej]

I think you're right that Codecov is diffing between current master and this branch. I take these reports with a grain of salt and only inspect them when I know I've added tests.