MRG: output bioboxes profile from tax metagenome (for CAMI)

[bluegenes]

Write bioboxes profiling format from tax metagenome, which can be used for CAMI submissions and comparisons.
The file produced by this output must have a .profile extension.

rendered sourmash bioboxes output format documentation

References:

• bioboxes format: https://github.com/bioboxes/rfc/blob/60263f34c57bc4137deeceec4c68a7f9f810f6a5/data-format/profiling.mkd
• luiz's gather_to_opal: see https://github.com/luizirber/2020-cami/blob/master/scripts/gather_to_opal.py
• luiz's early draft PR: https://github.com/sourmash-bio/sourmash/pull/1606/files

[codecov]

Codecov Report

Merging #2468 (ce4b8c4) into latest (827b897) will increase coverage by 0.04%.
The diff coverage is 98.21%.

@@            Coverage Diff             @@
##           latest    #2468      +/-   ##
==========================================
+ Coverage   92.64%   92.69%   +0.04%     
==========================================
  Files         104      104              
  Lines       12267    12321      +54     
  Branches     2279     2598     +319     
==========================================
+ Hits        11365    11421      +56     
+ Misses        599      598       -1     
+ Partials      303      302       -1     

Flag	Coverage Δ
python	92.69% <98.21%> (+0.04%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/sourmash/cli/utils.py	97.75% <75.00%> (-1.09%)	⬇️
src/sourmash/cli/tax/metagenome.py	100.00% <100.00%> (ø)
src/sourmash/tax/__main__.py	94.19% <100.00%> (+0.10%)	⬆️
src/sourmash/tax/tax_utils.py	98.34% <100.00%> (+0.05%)	⬆️

... and 9 files with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[luizirber]

(I think this will close #1606 too?)

[bluegenes]

@luizirber is there a reason you used Version:0.10.0 as compared with the 0.9.3 on https://github.com/bioboxes/rfc/blob/60263f34c57bc4137deeceec4c68a7f9f810f6a5/data-format/profiling.mkd?

[bluegenes]

@sourmash-bio/devs ready for review!

This PR is into #2469 for convenience /avoiding conflicts, but we should keep it separate and merge into latest after #2469 has been merged (that PR is huge and the functionality is distinct).

[ctb]

LGTM! nice!

[luizirber]

@luizirber is there a reason you used Version:0.10.0 as compared with the 0.9.3 on https://github.com/bioboxes/rfc/blob/60263f34c57bc4137deeceec4c68a7f9f810f6a5/data-format/profiling.mkd?

I don't remember... Probably because I was following the newest version I could find, but seems no tool ever implemented it...

PR describing the changes from 0.9 to 0.10: bioboxes/rfc#216

[bluegenes]

@dkoslicki does this fit requirements for CAMI intake?

[dkoslicki]

@dkoslicki does this fit requirements for CAMI intake?

Yes, that it does! It will make OPAL comparisons and the like much easier!