FIX: fix the infra-clade bug

q2_annotate/kraken2/select.py

@@ -262,7 +262,8 @@ def _kraken_to_ncbi_tree(df):
     while stack and parent_node.length == 0:
         _, parent_node = stack.pop()
 
-    if parent_node.children:
+    # Make sure we are not labeling infra-clades as actual tips
+    if parent_node.length == 1:
         parent_node.children[0].is_actual_tip = True
 
     return tree

q2_annotate/kraken2/tests/data/root-infraclade-report/0a2f080c-2774-4c64-a645-07660afc7eb4.report.txt

@@ -0,0 +1,18 @@
+100.00	180	0	R	1	root
+100.00	180	0	R1	131567	  cellular organisms
+100.00	180	0	R2	2	    Bacteria
+100.00	180	0	K	1783272	      Bacillati
+100.00	180	0	P	201174	        Actinomycetota
+100.00	180	0	C	84998	          Coriobacteriia
+ 99.44	179	0	O	84999	            Coriobacteriales
+ 99.44	179	0	F	84107	              Coriobacteriaceae
+ 99.44	179	0	G	102106	                Collinsella
+ 97.78	176	10	S	74426	                  Collinsella aerofaciens
+ 92.22	166	166	S1	411903	                    Collinsella aerofaciens ATCC 25986
+  1.67	3	0	G1	2637548	                  unclassified Collinsella
+  1.67	3	3	S	3132705	                    Collinsella sp. i05-0019-G5
+  0.56	1	0	O	1643822	            Eggerthellales
+  0.56	1	0	F	1643826	              Eggerthellaceae
+  0.56	1	0	G	644652	                Gordonibacter
+  0.56	1	0	S	471189	                  Gordonibacter pamelaeae
+  0.56	1	1	S1	657308	                    Gordonibacter pamelaeae 7-10-1-b

q2_annotate/kraken2/tests/data/root-infraclade-report/1acb175d-ddb0-410f-a513-7055cb90e706.report.txt

@@ -0,0 +1,4 @@
+ 50.00	1	1	U	0	unclassified
+ 50.00	1	0	R	1	root
+ 50.00	1	0	R1	131567	  cellular organisms
+ 50.00	1	1	R2	2	    Bacteria

q2_annotate/kraken2/tests/data/root-infraclade-report/f608b31a-c05c-4498-9e7d-67c89e33cabf.report.txt

@@ -0,0 +1,2 @@
+100.00	1	0	R	1	root
+100.00	1	1	R1	131567	  cellular organisms

q2_annotate/kraken2/tests/test_selection.py

@@ -7,24 +7,23 @@
 # ----------------------------------------------------------------------------
 import shutil
 import tempfile
-import unittest
 
 import pandas as pd
 import pandas.testing
-from pandas._testing import assert_frame_equal
 import skbio
+from pandas._testing import assert_frame_equal
+from q2_types.kraken2 import (
+    Kraken2OutputDirectoryFormat,
+    Kraken2ReportDirectoryFormat,
+)
+from qiime2.plugin.testing import TestPluginBase
+
 from q2_annotate.kraken2 import kraken2_to_features
 from q2_annotate.kraken2.select import (
-    _kraken_to_ncbi_tree,
     _find_lcas,
+    _kraken_to_ncbi_tree,
     kraken2_to_mag_features,
 )
-from qiime2.plugin.testing import TestPluginBase
-
-from q2_types.kraken2 import (
-    Kraken2ReportDirectoryFormat,
-    Kraken2OutputDirectoryFormat,
-)
 
 
 class MockTempDir(tempfile.TemporaryDirectory):
@@ -159,8 +158,7 @@ def test_kraken2_to_mag_features_incorrect_fraction_unclassified(self):
         hits = Kraken2OutputDirectoryFormat(self.get_data_path("outputs-mags"), "r")
         with self.assertRaisesRegex(
             ValueError,
-            "fraction for MAG '8894435a-c836-4c18-b475-8b38a9ab6c6b' "
-            "is not .* 99.01%",
+            "fraction for MAG '8894435a-c836-4c18-b475-8b38a9ab6c6b' is not .* 99.01%",
         ):
             kraken2_to_mag_features(reports, hits, 0.0)
 
@@ -245,7 +243,7 @@ def test_kraken2_to_mag_features_unclassified_no_add_up(self):
 
         with self.assertRaisesRegex(
             ValueError,
-            "fraction for MAG '8894435a-c836-4c18-b475-8b38a9ab6c6b' " "is not 100.0",
+            "fraction for MAG '8894435a-c836-4c18-b475-8b38a9ab6c6b' is not 100.0",
         ):
             kraken2_to_mag_features(reports, hits, 0.1)
 
@@ -380,7 +378,8 @@ def test_find_lcas_mode_lca_all_unclassified(self):
     #     pandas.testing.assert_frame_equal(obs, exp)
 
 
-class TestKrakenSelectEdgeCases(unittest.TestCase):
+class TestKrakenSelectEdgeCases(TestPluginBase):
+    package = "q2_annotate.kraken2.tests"
 
     def make_dirfmt(self, string, coverage=False):
         """
@@ -464,7 +463,6 @@ def test_kraken_to_ncbi_tree_no_tricks(self):
         )
 
         table, taxonomy = kraken2_to_features(dirfmt)
-
         pandas.testing.assert_frame_equal(exp_table, table)
         pandas.testing.assert_frame_equal(exp_tax, taxonomy)
 
@@ -608,3 +606,13 @@ def test_kraken_to_ncbi_tree_rankless_domain_inference(self):
 
         pandas.testing.assert_frame_equal(exp_table, table)
         pandas.testing.assert_frame_equal(exp_tax, taxonomy)
+
+    def test_kraken2_to_features_root_infraclades(self):
+        """
+        Tests that root infra-clades are not treated as actual tips leading
+        to mismatch between feature table and taxonomy.
+        """
+        reports = Kraken2ReportDirectoryFormat(
+            self.get_data_path("root-infraclade-report"), "r"
+        )
+        kraken2_to_features(reports)