MRG: Fix tax metagenome to work on gather output created with `--es…

…timate-ani-ci` (#2952)

The `tax metagenome` code errors out with a confusing error message when
gather results containing confidence intervals for the ANI calculations
are output. This PR adds a test and fixes the problem.

## Details

The error message is:
```
ERROR: '/var/folders/6s/_f373w1d6hdfjc2kjstq97s80000gp/T/sourmashtest_rs5l3b23/gather.csv' is missing columns needed for taxonomic summarization. Please run gather with sourmash >= 4.4.
```

and it is caused by `GatherRow` running across the various extra columns
added by `--estimate-ani-ci`, such as `query_containment_ani_low`.

The fix is to add these columns in as optional/unused columns in the
`GatherRow` dataclass.

src/sourmash/tax/tax_utils.py

@@ -1540,6 +1540,10 @@ class GatherRow:
     n_unique_weighted_found: int = None
     sum_weighted_found: int = None
     total_weighted_hashes: int = None
+    query_containment_ani_low: float = None
+    query_containment_ani_high: float = None
+    match_containment_ani_low: float = None
+    match_containment_ani_high: float = None
 
 
 @dataclass

tests/test_tax.py

@@ -2201,6 +2201,49 @@ def test_genome_ani_lemonade_classify(runtmp):
     assert 'MAG3_1,d__Bacteria,p__Bacteroidota,c__Chlorobia,o__Chlorobiales,f__Chlorobiaceae,g__Prosthecochloris,s__Prosthecochloris vibrioformis' in output
 
 
+def test_genome_ani_lemonade_classify_estimate_ani_ci(runtmp):
+    # test a complete MAG classification with lemonade MAG from STAMPS 2022
+    # (real data!)
+    c = runtmp
+
+    ## first run gather
+    genome = utils.get_test_data('tax/lemonade-MAG3.sig.gz')
+    matches = utils.get_test_data('tax/lemonade-MAG3.x.gtdb.matches.zip')
+
+    c.run_sourmash('gather', genome, matches,
+                   '--threshold-bp=5000', '-o', 'gather.csv', '--estimate-ani')
+
+    print(c.last_result.status)
+    print(c.last_result.out)
+    print(c.last_result.err)
+
+    assert c.last_result.status == 0
+
+    this_gather_file = c.output('gather.csv')
+    this_gather = Path(this_gather_file).read_text().splitlines()
+
+    assert len(this_gather) == 4
+
+    ## now run 'tax genome' with human output
+    taxonomy_file = utils.get_test_data('tax/lemonade-MAG3.x.gtdb.matches.tax.csv')
+    c.run_sourmash('tax', 'genome', '-g', this_gather_file, '-t', taxonomy_file,
+                   '--ani', '0.8', '-F', 'human')
+
+    output = c.last_result.out
+    assert 'MAG3_1            match     5.3%     91.0%  d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris;s__Prosthecochloris vibrioformis' in output
+
+    # aaand classify to lineage_csv
+    c.run_sourmash('tax', 'genome', '-g', this_gather_file, '-t', taxonomy_file,
+                   '--ani', '0.8', '-F', 'lineage_csv')
+
+    print(c.last_result.status)
+    print(c.last_result.out)
+    print(c.last_result.err)
+    output = c.last_result.out
+    assert 'ident,superkingdom,phylum,class,order,family,genus,species' in output
+    assert 'MAG3_1,d__Bacteria,p__Bacteroidota,c__Chlorobia,o__Chlorobiales,f__Chlorobiaceae,g__Prosthecochloris,s__Prosthecochloris vibrioformis' in output
+
+
 def test_metagenome_no_gather_csv(runtmp):
     # test tax metagenome with no -g
     taxonomy_file = utils.get_test_data('tax/lemonade-MAG3.x.gtdb.matches.tax.csv')