Replacing superkingdom with domain (#178)

crosenth · web-flow · commit 1eca99f320d5 · 2025-06-10T13:33:11.000-07:00
* Replacing superkingdom with domain

* updated test cases with new ranks
diff --git a/taxtastic/subcommands/lineage_table.py b/taxtastic/subcommands/lineage_table.py
@@ -29,7 +29,7 @@
     ('order', 'o'),
     ('class', 'c'),
     ('phylum', 'p'),
-    ('superkingdom', 'k'),
+    ('domain', 'd'),
 
   Lineages are truncated to either the most specific defined rank or
   species, and missing tax_names at a given rank are replaced with the
@@ -122,7 +122,7 @@ def action(args):
             ('order', 'o'),
             ('class', 'c'),
             ('phylum', 'p'),
-            ('superkingdom', 'k'),
+            ('domain', 'd'),
         ]
 
         def clean(tax_name, rexp=re.compile(r'[^-A-Z0-9_\[\]]+', re.I)):
diff --git a/testfiles/lactobacillus2-0.2.refpkg/CONTENTS.json b/testfiles/lactobacillus2-0.2.refpkg/CONTENTS.json
@@ -12,9 +12,9 @@
   "md5": {
     "profile": "7b36841cae1db2a2c4d60ea44db4aba9", 
     "phylo_model": "f288a37a50b2a113110185fbc8f48028", 
-    "taxonomy": "9bc2edc9c67801c4a9acd7e166144f4a", 
+    "taxonomy": "09fe0f3f9bc813154af0e42ce4b6645d", 
     "tree": "2f11faa616fc7f04d7694436b5cca05f", 
-    "aln_fasta": "fd8a198c0215f3577f9b083da87128bb", 
+    "aln_fasta": "ff1fa6a07a090b96c2f77f8449010331", 
     "seq_info": "230bfb5a78075a012e114bef635a4b18", 
     "aln_sto": "6420db16bded3a5b119b16e2972be66e", 
     "tree_stats": "2e57e7e56708f4b31db8025ef99722ef"
diff --git a/testfiles/lactobacillus2-0.2.refpkg/chosen.fasta b/testfiles/lactobacillus2-0.2.refpkg/chosen.fasta
diff --git a/testfiles/lactobacillus2-0.2.refpkg/taxtable.csv b/testfiles/lactobacillus2-0.2.refpkg/taxtable.csv
@@ -1,7 +1,7 @@
-"tax_id","parent_id","rank","tax_name","root","below_root","superkingdom","phylum","class","order","family","genus","species_group","species"
+"tax_id","parent_id","rank","tax_name","root","cellular_root","domain","phylum","class","order","family","genus","species_group","species"
 "1","1","root","root","1","","","","","","","","",""
-"131567","1","below_root","cellular organisms","1","131567","","","","","","","",""
-"2","131567","superkingdom","Bacteria","1","131567","2","","","","","","",""
+"131567","1","cellular_root","cellular organisms","1","131567","","","","","","","",""
+"2","131567","domain","Bacteria","1","131567","2","","","","","","",""
 "1239","2","phylum","Firmicutes","1","131567","2","1239","","","","","",""
 "1224","2","phylum","Proteobacteria","1","131567","2","1224","","","","","",""
 "91061","1239","class","Bacilli","1","131567","2","1239","91061","","","","",""
diff --git a/testfiles/minimal_taxonomy.csv b/testfiles/minimal_taxonomy.csv
@@ -1,7 +1,7 @@
-"tax_id","parent_id","rank","tax_name","root","below_root","superkingdom","phylum","class","order","family","genus","species"
+"tax_id","parent_id","rank","tax_name","root","cellular_root","domain","phylum","class","order","family","genus","species"
 "1","1","root","root","1","","","","","","","",""
-"131567","1","below_root","cellular organisms","1","131567","","","","","","",""
-"2","131567","superkingdom","Bacteria","1","131567","2","","","","","",""
+"131567","1","cellular_root","cellular organisms","1","131567","","","","","","",""
+"2","131567","domain","Bacteria","1","131567","2","","","","","",""
 "1239","2","phylum","Firmicutes","1","131567","2","1239","","","","",""
 "91061","1239","class","Bacilli","1","131567","2","1239","91061","","","",""
 "186826","91061","order","Lactobacillales","1","131567","2","1239","91061","186826","","",""
diff --git a/testfiles/simple_taxtable.csv b/testfiles/simple_taxtable.csv
@@ -1,7 +1,7 @@
-"tax_id","parent_id","rank","tax_name","root","below_root","superkingdom","superphylum","phylum","subphylum","class","subclass","order","below_order","below_below_order","suborder","family","below_family","genus","subgenus","species_group","species","below_species","below_below_species","subspecies","below_subspecies"
+"tax_id","parent_id","rank","tax_name","root","cellular_root","domain","superphylum","phylum","subphylum","class","subclass","order","below_order","below_below_order","suborder","family","below_family","genus","subgenus","species_group","species","below_species","below_below_species","subspecies","below_subspecies"
 "1","1","root","root","1","","","","","","","","","","","","","","","","","","","","",""
-"131567","1","below_root","cellular organisms","1","131567","","","","","","","","","","","","","","","","","","","",""
-"2","131567","superkingdom","Bacteria","1","131567","2","","","","","","","","","","","","","","","","","","",""
+"131567","1","cellular_root","cellular organisms","1","131567","","","","","","","","","","","","","","","","","","","",""
+"2","131567","domain","Bacteria","1","131567","2","","","","","","","","","","","","","","","","","","",""
 "68336","2","superphylum","Bacteroidetes/Chlorobi group","1","131567","2","68336","","","","","","","","","","","","","","","","","",""
 "201174","2","phylum","Actinobacteria","1","131567","2","","201174","","","","","","","","","","","","","","","","",""
 "976","68336","phylum","Bacteroidetes","1","131567","2","68336","976","","","","","","","","","","","","","","","","",""
diff --git a/testfiles/small_taxonomy.db b/testfiles/small_taxonomy.db
diff --git a/testfiles/tax_table.csv b/testfiles/tax_table.csv
@@ -1,9 +1,9 @@
-"tax_id","parent_id","rank","tax_name","root","below_root","superkingdom","below_superkingdom","below_below_superkingdom","superphylum","phylum","class","subclass","order","below_order","below_below_order","suborder","family","below_family","genus","species_group","species_subgroup","species","below_species"
+"tax_id","parent_id","rank","tax_name","root","cellular_root","domain","below_domain","below_below_domain","superphylum","phylum","class","subclass","order","below_order","below_below_order","suborder","family","below_family","genus","species_group","species_subgroup","species","below_species"
 "1","1","root","root","1","","","","","","","","","","","","","","","","","","",""
-"131567","1","below_root","cellular organisms","1","131567","","","","","","","","","","","","","","","","","",""
-"2","131567","superkingdom","Bacteria","1","131567","2","","","","","","","","","","","","","","","","",""
-"2323","2","below_superkingdom","unclassified Bacteria","1","131567","2","2323","","","","","","","","","","","","","","","",""
-"95818","2323","below_below_superkingdom","candidate division TM7","1","131567","2","2323","95818","","","","","","","","","","","","","","",""
+"131567","1","cellular_root","cellular organisms","1","131567","","","","","","","","","","","","","","","","","",""
+"2","131567","domain","Bacteria","1","131567","2","","","","","","","","","","","","","","","","",""
+"2323","2","below_domain","unclassified Bacteria","1","131567","2","2323","","","","","","","","","","","","","","","",""
+"95818","2323","below_below_domain","candidate division TM7","1","131567","2","2323","95818","","","","","","","","","","","","","","",""
 "68336","2","superphylum","Bacteroidetes/Chlorobi group","1","131567","2","","","68336","","","","","","","","","","","","","",""
 "201174","2","phylum","Actinobacteria","1","131567","2","","","","201174","","","","","","","","","","","","",""
 "976","68336","phylum","Bacteroidetes","1","131567","2","","","68336","976","","","","","","","","","","","","",""
diff --git a/testfiles/taxdmp.zip b/testfiles/taxdmp.zip
diff --git a/testfiles/taxids1.taxtable b/testfiles/taxids1.taxtable
@@ -1,7 +1,7 @@
-"tax_id","parent_id","rank","tax_name","root","below_root","superkingdom","superphylum","phylum","class","subclass","order","below_order","suborder","family","genus","species"
+"tax_id","parent_id","rank","tax_name","root","cellular_root","domain","superphylum","phylum","class","subclass","order","below_order","suborder","family","genus","species"
 "1","1","root","root","1","","","","","","","","","","","",""
-"131567","1","below_root","cellular organisms","1","131567","","","","","","","","","","",""
-"2","131567","superkingdom","Bacteria","1","131567","2","","","","","","","","","",""
+"131567","1","cellular_root","cellular organisms","1","131567","","","","","","","","","","",""
+"2","131567","domain","Bacteria","1","131567","2","","","","","","","","","",""
 "68336","2","superphylum","Bacteroidetes/Chlorobi group","1","131567","2","68336","","","","","","","","",""
 "201174","2","phylum","Actinobacteria","1","131567","2","","201174","","","","","","","",""
 "976","68336","phylum","Bacteroidetes","1","131567","2","68336","976","","","","","","","",""
diff --git a/tests/test_taxit.py b/tests/test_taxit.py
@@ -129,7 +129,7 @@ def test_all_ranks(self):
         with open(self.outfile, **self.openargs) as fp:
             self.assertEqual("""tax_name,tax_id,rank
 Bacilli,91061,class
-Bacteria,2,superkingdom
+Bacteria,2,domain
 Enterobacteriaceae,543,family
 Enterobacteriales,91347,order
 Escherichia,561,genus
@@ -138,7 +138,7 @@ def test_all_ranks(self):
 Lactobacillaceae,33958,family
 Lactobacillales,186826,order
 Lactobacillus,1578,genus
-cellular organisms,131567,below_root
+cellular organisms,131567,cellular_root
 """, fp.read())
 
     def test_species(self):
diff --git a/tests/test_taxonomy.py b/tests/test_taxonomy.py
@@ -385,12 +385,15 @@ def test_is_below(self):
         self.assertFalse(self.tax.is_below('kingdom', 'family'))
         self.assertEqual(
             self.tax.ranks_below('species'),
-            ['forma', 'varietas', 'subspecies'])
+            ['forma', 'subvariety', 'varietas', 'serogroup',
+             'pathogroup', 'morph', 'genotype', 'biotype', 'subspecies'])
         self.assertEqual(
             self.tax.ranks_below('family'),
-            ['forma', 'varietas', 'subspecies', 'species',
-             'species_subgroup', 'species_group', 'subgenus',
-             'genus', 'subtribe', 'tribe', 'subfamily'])
+            ['forma', 'subvariety', 'varietas', 'serogroup', 'pathogroup',
+             'morph', 'genotype', 'biotype', 'subspecies', 'species',
+             'species_subgroup', 'species_group', 'subseries', 'series',
+             'subsection', 'section', 'subgenus', 'genus', 'subtribe',
+             'tribe', 'subfamily'])
 
     def test_nary_subtree(self):
         self.assertRaises(ValueError, self.tax.nary_subtree, None)
diff --git a/tests/test_taxtable.py b/tests/test_taxtable.py
@@ -34,10 +34,10 @@ def test_lineage(self):
                          [i.tax_id for i in lineage])
 
     def test_write_taxtable(self):
-        expected = '''"tax_id","parent_id","rank","tax_name","root","below_root","superkingdom","phylum","class","order","family","genus","species"
+        expected = '''"tax_id","parent_id","rank","tax_name","root","cellular_root","domain","phylum","class","order","family","genus","species"
 "1","1","root","root","1","","","","","","","",""
-"131567","1","below_root","cellular organisms","1","131567","","","","","","",""
-"2","131567","superkingdom","Bacteria","1","131567","2","","","","","",""
+"131567","1","cellular_root","cellular organisms","1","131567","","","","","","",""
+"2","131567","domain","Bacteria","1","131567","2","","","","","",""
 "1239","2","phylum","Firmicutes","1","131567","2","1239","","","","",""
 "91061","1239","class","Bacilli","1","131567","2","1239","91061","","","",""
 "186826","91061","order","Lactobacillales","1","131567","2","1239","91061","186826","","",""
