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Merged
crosenth merged 2 commits into from
Jun 10, 2025
Merged

Replacing superkingdom with domain #178

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6cdfd95
Replacing superkingdom with domain
crosenth May 29, 2025
e7f20dd
updated test cases with new ranks
crosenth May 29, 2025
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4 changes: 2 additions & 2 deletions taxtastic/subcommands/lineage_table.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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)):
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4 changes: 2 additions & 2 deletions testfiles/lactobacillus2-0.2.refpkg/CONTENTS.json
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Expand Up @@ -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"
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92 changes: 46 additions & 46 deletions testfiles/lactobacillus2-0.2.refpkg/chosen.fasta
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6 changes: 3 additions & 3 deletions testfiles/lactobacillus2-0.2.refpkg/taxtable.csv
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Original file line number Diff line number Diff line change
@@ -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","","","","",""
Expand Down
6 changes: 3 additions & 3 deletions testfiles/minimal_taxonomy.csv
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@@ -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","","",""
Expand Down
6 changes: 3 additions & 3 deletions testfiles/simple_taxtable.csv
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@@ -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","","","","","","","","","","","","","","","","",""
Expand Down
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10 changes: 5 additions & 5 deletions testfiles/tax_table.csv
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@@ -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","","","","","","","","","","","","",""
Expand Down
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6 changes: 3 additions & 3 deletions testfiles/taxids1.taxtable
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Original file line number Diff line number Diff line change
@@ -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","","","","","","","",""
Expand Down
4 changes: 2 additions & 2 deletions tests/test_taxit.py
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Expand Up @@ -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
Expand All @@ -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):
Expand Down
11 changes: 7 additions & 4 deletions tests/test_taxonomy.py
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Expand Up @@ -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)
Expand Down
6 changes: 3 additions & 3 deletions tests/test_taxtable.py
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Expand Up @@ -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","","",""
Expand Down