cleanup; add test for multiple

src/sourmash/tax/__main__.py

@@ -453,8 +453,9 @@ def summarize(args):
 
     notify(f"...loaded {len(tax_assign)} entries.")
 
-    print_results(f"num idents: {len(tax_assign)}")
+    print_results(f"number of distinct taxonomic lineages: {len(tax_assign)}")
 
+    # count the number of distinct lineage names seen
     rank_counts = defaultdict(int)
     name_seen = set()
     for v in tax_assign.values():
@@ -464,19 +465,11 @@ def summarize(args):
                 rank_counts[rank] += 1
                 name_seen.add(name)
 
-            if 0:
-                # @CTB
-                # check duplicates?
-                sofar.append(name)
-                tup = tuple(sofar)
-                seen.add(tuple(sofar))
-        #break
-
     rank_count_items = list(rank_counts.items())
     rank_count_items.sort(key=lambda x: x[1])
     for rank, count in rank_count_items:
         rank_name_str = f"{rank}:"
-        print_results(f"rank {rank_name_str:<20s} {count} distinct identifiers")
+        print_results(f"rank {rank_name_str:<20s} {count} distinct taxonomic lineages")
 
     if args.output_lineage_information:
         notify("now calculating detailed lineage counts...")

tests/test_tax.py

@@ -2982,14 +2982,34 @@ def test_tax_summarize(runtmp):
     out = runtmp.last_result.out
     err = runtmp.last_result.err
 
-    assert "num idents: 6" in out
-    assert "rank superkingdom:        1 distinct identifiers" in out
-    assert "rank phylum:              2 distinct identifiers" in out
-    assert "rank class:               2 distinct identifiers" in out
-    assert "rank order:               2 distinct identifiers" in out
-    assert "rank family:              3 distinct identifiers" in out
-    assert "rank genus:               4 distinct identifiers" in out
-    assert "rank species:             4 distinct identifiers" in out
+    assert "number of distinct taxonomic lineages: 6" in out
+    assert "rank superkingdom:        1 distinct taxonomic lineages" in out
+    assert "rank phylum:              2 distinct taxonomic lineages" in out
+    assert "rank class:               2 distinct taxonomic lineages" in out
+    assert "rank order:               2 distinct taxonomic lineages" in out
+    assert "rank family:              3 distinct taxonomic lineages" in out
+    assert "rank genus:               4 distinct taxonomic lineages" in out
+    assert "rank species:             4 distinct taxonomic lineages" in out
+
+
+def test_tax_summarize_multiple(runtmp):
+    # test basic operation with summarize on multiple files
+    tax1 = utils.get_test_data('tax/bacteria_refseq_lineage.csv')
+    tax2 = utils.get_test_data('tax/protozoa_genbank_lineage.csv')
+
+    runtmp.sourmash('tax', 'summarize', tax1, tax2)
+
+    out = runtmp.last_result.out
+    err = runtmp.last_result.err
+
+    assert "number of distinct taxonomic lineages: 6" in out
+    assert "rank superkingdom:        2 distinct taxonomic lineages" in out
+    assert "rank phylum:              3 distinct taxonomic lineages" in out
+    assert "rank class:               4 distinct taxonomic lineages" in out
+    assert "rank order:               4 distinct taxonomic lineages" in out
+    assert "rank family:              5 distinct taxonomic lineages" in out
+    assert "rank genus:               5 distinct taxonomic lineages" in out
+    assert "rank species:             5 distinct taxonomic lineages" in out
 
 
 def test_tax_summarize_empty_line(runtmp):
@@ -3001,14 +3021,14 @@ def test_tax_summarize_empty_line(runtmp):
     out = runtmp.last_result.out
     err = runtmp.last_result.err
 
-    assert "num idents: 6" in out
-    assert "rank superkingdom:        1 distinct identifiers" in out
-    assert "rank phylum:              2 distinct identifiers" in out
-    assert "rank class:               2 distinct identifiers" in out
-    assert "rank order:               2 distinct identifiers" in out
-    assert "rank family:              3 distinct identifiers" in out
-    assert "rank genus:               4 distinct identifiers" in out
-    assert "rank species:             4 distinct identifiers" in out
+    assert "number of distinct taxonomic lineages: 6" in out
+    assert "rank superkingdom:        1 distinct taxonomic lineages" in out
+    assert "rank phylum:              2 distinct taxonomic lineages" in out
+    assert "rank class:               2 distinct taxonomic lineages" in out
+    assert "rank order:               2 distinct taxonomic lineages" in out
+    assert "rank family:              3 distinct taxonomic lineages" in out
+    assert "rank genus:               4 distinct taxonomic lineages" in out
+    assert "rank species:             4 distinct taxonomic lineages" in out
 
 
 def test_tax_summarize_empty(runtmp):
@@ -3032,7 +3052,7 @@ def test_tax_summarize_csv(runtmp):
     out = runtmp.last_result.out
     err = runtmp.last_result.err
 
-    assert "num idents: 6" in out
+    assert "number of distinct taxonomic lineages: 6" in out
     assert "saved 18 lineage counts to 'ranks.csv'" in err
 
     csv_out = runtmp.output('ranks.csv')
@@ -3074,14 +3094,14 @@ def test_tax_summarize_on_annotate(runtmp):
     print(out)
     print(err)
 
-    assert "num idents: 4" in out
-    assert "rank superkingdom:        1 distinct identifiers" in out
-    assert "rank phylum:              2 distinct identifiers" in out
-    assert "rank class:               2 distinct identifiers" in out
-    assert "rank order:               2 distinct identifiers" in out
-    assert "rank family:              2 distinct identifiers" in out
-    assert "rank genus:               3 distinct identifiers" in out
-    assert "rank species:             3 distinct identifiers" in out
+    assert "number of distinct taxonomic lineages: 4" in out
+    assert "rank superkingdom:        1 distinct taxonomic lineages" in out
+    assert "rank phylum:              2 distinct taxonomic lineages" in out
+    assert "rank class:               2 distinct taxonomic lineages" in out
+    assert "rank order:               2 distinct taxonomic lineages" in out
+    assert "rank family:              2 distinct taxonomic lineages" in out
+    assert "rank genus:               3 distinct taxonomic lineages" in out
+    assert "rank species:             3 distinct taxonomic lineages" in out
 
 
 def test_tax_summarize_strain_csv(runtmp):
@@ -3093,7 +3113,7 @@ def test_tax_summarize_strain_csv(runtmp):
     out = runtmp.last_result.out
     err = runtmp.last_result.err
 
-    assert "num idents: 6" in out
+    assert "number of distinct taxonomic lineages: 6" in out
     assert "saved 24 lineage counts to 'ranks.csv'" in err
 
     csv_out = runtmp.output('ranks.csv')
@@ -3132,7 +3152,7 @@ def test_tax_summarize_strain_csv_with_lineages(runtmp):
     out = runtmp.last_result.out
     err = runtmp.last_result.err
 
-    assert "num idents: 6" in out
+    assert "number of distinct taxonomic lineages: 6" in out
     assert "saved 24 lineage counts to" in err
 
     csv_out = runtmp.output('ranks.csv')