[MRG] revise sourmash tax user experience and output formats

[ctb]

Miscellaneous sourmash tax UX tidying, motivated by STAMPS 2022 tutorial.

Please see the updated tutorial, added to this PR, here.

This PR:

• adds -F as a synonym for --output-format to tax metagenome and tax genome
• adds -F human as a type of output format to tax metagenome and tax genome
• adds -F lineage_csv as output format for tax metagenome (see tax genome should directly support lineage CSVs as an output format #2153)
• quotes output filenames in error messages
• only outputs information about missing lineages when there are some :)
• switches to using forward quotes instead of backquotes for format output message

Fixes #2153

TODO:

• add, like, tests, maaaan
• add headers
• create issue to change default output to human for sourmash v5?
• add (adjusted) tutorial?
• 'human' output filenames - should we add anything to them, similarly to 'krona.tsv'?
• revisit hackmd formatting...

[codecov]

Codecov Report

Merging #2158 (a83ff3b) into latest (2f38f6c) will increase coverage by 0.08%.
The diff coverage is 98.73%.

@@            Coverage Diff             @@
##           latest    #2158      +/-   ##
==========================================
+ Coverage   84.34%   84.43%   +0.08%     
==========================================
  Files         130      130              
  Lines       15320    15370      +50     
  Branches     2176     2192      +16     
==========================================
+ Hits        12922    12978      +56     
+ Misses       2095     2092       -3     
+ Partials      303      300       -3     

Flag	Coverage Δ
python	91.81% <98.73%> (+0.09%)	⬆️
rust	65.29% <ø> (ø)

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

Impacted Files	Coverage Δ
src/sourmash/tax/__main__.py	88.47% <95.45%> (+0.49%)	⬆️
src/sourmash/cli/tax/annotate.py	100.00% <100.00%> (+10.52%)	⬆️
src/sourmash/cli/tax/genome.py	90.32% <100.00%> (+6.45%)	⬆️
src/sourmash/cli/tax/metagenome.py	89.28% <100.00%> (+7.14%)	⬆️
src/sourmash/tax/tax_utils.py	98.08% <100.00%> (+0.13%)	⬆️

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[ctb]

@bluegenes what do you think of the new human-readable format?

I made a new copy of the STAMPS 2022 tutorial and updated the sourmash tax commands there - https://hackmd.io/vr6BT3mdQKWdlXEqcLUnZg?view. The necessary signatures are attached to this comment in a zip, if you want to give it a try!
stamps2022-files.zip

[bluegenes]

column headers would be helpful for printed output! otherwise looking better!

[ctb]

@bluegenes should we use ANI in the human-readable output? Or add ANI in there? Seems like a good idea...

[bluegenes]

@bluegenes should we use ANI in the human-readable output? Or add ANI in there? Seems like a good idea...

At minimum, we should provide it for tax genome results!

[ctb]

done! example output -

sample name    proportion   ANI    lineage
-----------    ----------   ---    -------
MAG3_1             5.3%     91.0%  d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris;s__Prosthecochloris vibrioformis
MAG2_1             5.0%     90.8%  d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum;s__Chlorobaculum parvum_B
MAG1_1             1.1%     86.5%  d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA1568;g__JAAXTX01;s__JAAXTX01 sp013334245

[ctb]

Ready for review & merge, but no hurry @bluegenes

[bluegenes]

sample name proportion ANI lineage

should we call this cANI (for "containment ANI"), as I'm using for the writeup?

[ctb]

Fixed - ready for review & merge @bluegenes !

[bluegenes]

human readable format is v helpful and tutorial is great!

some suggested changes, otherwise good

[ctb]

@bluegenes re the two remaining comments about classifying at a specific rank, I'm worried I don't understand the code well enough to be sure of what's going on :). I'll take a look in more detail and either resolve the comments or amplify on them with a clearer question before I merge, unless you get a chance to dig into the code and reassure me that I'm not messing anything up here.