add tax summarize

[ctb]

This PR adds a tax summarize command per #2212.

It also:

• tackles native loading of with-lineages files produced by tax annotate as taxonomy spreadsheets (provide taxonomy operations that work on semicolon-separated lineages #2185)
• improves error reporting output for wonky unicode formatted tax CSV files for sourmash tax prepare fails with No taxonomic identifiers found. #2326

Tackles #2212
Tackles #2185
Tackles parts of #2326

TODO

• tests!
• docs!
• check desired output format against christy e-mail
• provide "linting" style output? - punted to add tax crosscheck to compare databases and lineages for correctness #2361
• maybe we want to use this command, or a separate command, to compare b/t a set of signatures (or a manifest...) and a set of taxonomies? e.g. tax crosscheck --db db --taxonomy <taxonomy> that will tell us which identifiers don't have taxonomy, and which taxonomy entries don't have sketches? - punted to add tax crosscheck to compare databases and lineages for correctness #2361

Example output

Running on a traditional taxonomy file:

% sourmash tax summarize gtdb-rs202.taxonomy.v2.db                      

== This is sourmash version 4.5.0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

loading taxonomies...
...loaded 258406 entries.
num idents: 258406
rank superkingdom:        2 distinct identifiers
rank phylum:              169 distinct identifiers
rank class:               419 distinct identifiers
rank order:               1312 distinct identifiers
rank family:              3264 distinct identifiers
rank genus:               12888 distinct identifiers
rank species:             47894 distinct identifiers

On a gather-with-lineages file:

% sourmash tax summarize SRR606249-k31.x.gtdb.gather.with-lineages.csv                   

== This is sourmash version 4.5.0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

loading taxonomies...
...loaded 84 entries.
num idents: 84
rank superkingdom:        2 distinct identifiers
rank phylum:              25 distinct identifiers
rank class:               32 distinct identifiers
rank order:               42 distinct identifiers
rank family:              52 distinct identifiers
rank genus:               60 distinct identifiers
rank species:             84 distinct identifiers

On the bad CSV file from #2326 -

% sourmash tax summarize /Users/t/Downloads/cheesegenomes.lineages.csv

== This is sourmash version 4.5.0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

loading taxonomies...
ERROR while loading taxonomies!
cannot read taxonomy assignments from '/Users/t/Downloads/cheesegenomes.lineages.csv': No taxonomic identifiers found; headers are '\ufeffident','taxid','superkingdom','phylum','class','order','family','genus','species','strain'

CSV output of per-rank information

With CSV output,

% sourmash tax summarize gtdb-rs207.taxonomy.sqldb -o aaa.csv

== This is sourmash version 4.5.0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

loading taxonomies...
...loaded 317542 entries.
num idents: 317542
rank superkingdom:        2 distinct identifiers
rank phylum:              189 distinct identifiers
rank class:               481 distinct identifiers
rank order:               1593 distinct identifiers
rank family:              4107 distinct identifiers
rank genus:               16686 distinct identifiers
rank species:             65703 distinct identifiers
now calculating detailed lineage counts...
...done!
saved 88761 lineage counts to 'aaa.csv'

and aaa.csv looks like:

	rank	count	lineage
0	superkingdom	311480	d__Bacteria
1	phylum	141114	d__Bacteria;p__Proteobacteria
2	class	121804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria
3	order	74108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales
4	family	63971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae
5	phylum	61795	d__Bacteria;p__Firmicutes
6	class	61794	d__Bacteria;p__Firmicutes;c__Bacilli
7	order	32177	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales
8	phylum	28532	d__Bacteria;p__Actinobacteriota
9	genus	27205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia

[codecov]

Codecov Report

Merging #2333 (43e094d) into latest (502f668) will increase coverage by 0.08%.
The diff coverage is 95.83%.

@@            Coverage Diff             @@
##           latest    #2333      +/-   ##
==========================================
+ Coverage   83.98%   84.06%   +0.08%     
==========================================
  Files         129      130       +1     
  Lines       14969    15059      +90     
  Branches     2192     2212      +20     
==========================================
+ Hits        12572    12660      +88     
  Misses       2103     2103              
- Partials      294      296       +2     

Flag	Coverage Δ
python	92.18% <95.83%> (+0.04%)	⬆️
rust	57.73% <ø> (ø)

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

Impacted Files	Coverage Δ
src/sourmash/tax/tax_utils.py	98.11% <91.80%> (-0.21%)	⬇️
src/sourmash/cli/tax/__init__.py	100.00% <100.00%> (ø)
src/sourmash/cli/tax/summarize.py	100.00% <100.00%> (ø)
src/sourmash/tax/__main__.py	93.64% <100.00%> (+1.00%)	⬆️

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[ctb]

ready for review @bluegenes !

[bluegenes]

lgtm!!