update sytanx for new test

etetoolkit · May 30, 2024 · c1533ac · c1533ac
1 parent 7739f27
commit c1533ac
Showing 1 changed file with 15 additions and 15 deletions.
diff --git a/tests/test_ncbiquery.py b/tests/test_ncbiquery.py
@@ -164,33 +164,33 @@ def test_get_topology():
 def test_merged_id():
     ncbi = NCBITaxa(dbfile=DATABASE_PATH)
     t1 = ncbi.get_lineage(649756)
-    self.assertEqual(t1, [1, 131567, 2, 1783272, 1239, 186801, 3085636, 186803, 207244, 649756])
+    assert t1 == [1, 131567, 2, 1783272, 1239, 186801, 3085636, 186803, 207244, 649756]
     t2 = ncbi.get_lineage("649756")
-    self.assertEqual(t2, [1, 131567, 2, 1783272, 1239, 186801, 3085636, 186803, 207244, 649756])
+    assert t2 == [1, 131567, 2, 1783272, 1239, 186801, 3085636, 186803, 207244, 649756]
+
 
 def test_ignore_unclassified():
     # normal case
     tree = PhyloTree('((9606, 9598), 10090);')
     tree.annotate_ncbi_taxa(taxid_attr='name', ignore_unclassified=False)
-    self.assertEqual(tree.common_ancestor(['9606', '9598']).props.get("sci_name"), 'Homininae')
-    self.assertEqual(tree.common_ancestor(['9606', '10090']).props.get("sci_name"), 'Euarchontoglires')
 
+    assert tree.common_ancestor(['9606', '9598']).props.get("sci_name") == 'Homininae'
+    assert tree.common_ancestor(['9606', '10090']).props.get("sci_name") == 'Euarchontoglires'
+
     # empty case
     tree = PhyloTree('((9606, sample1), 10090);')
     tree.annotate_ncbi_taxa(taxid_attr='name', ignore_unclassified=False)
-    self.assertEqual(tree.common_ancestor(['9606', 'sample1']).props.get("sci_name"), '')
-    self.assertEqual(tree.common_ancestor(['9606', 'sample1']).props.get("rank"), 'Unknown')
-    self.assertEqual(tree.common_ancestor(['9606', '10090']).props.get("sci_name"), '')
-
+
+    assert tree.common_ancestor(['9606', 'sample1']).props.get("sci_name") == ''
+    assert tree.common_ancestor(['9606', 'sample1']).props.get("rank") == 'Unknown'
+    assert tree.common_ancestor(['9606', '10090']).props.get("sci_name") == ''
+
     # ignore unclassified
     tree = PhyloTree('((9606, sample1), 10090);')
     tree.annotate_ncbi_taxa(taxid_attr='name', ignore_unclassified=True)
-    self.assertEqual(tree.common_ancestor(['9606', 'sample1']).props.get("sci_name"), 'Homo sapiens')
-    self.assertEqual(tree.common_ancestor(['9606', 'sample1']).props.get("rank"), 'species')
-    self.assertEqual(tree.common_ancestor(['9606', '10090']).props.get("sci_name"), 'Euarchontoglires')
 
-    t1 = ncbi.get_lineage(649756)
-    assert t1 == [1, 131567, 2, 1783272, 1239, 186801, 3085636, 186803, 207244, 649756]
+    assert tree.common_ancestor(['9606', 'sample1']).props.get("sci_name") == 'Homo sapiens'
+    assert tree.common_ancestor(['9606', 'sample1']).props.get("rank") == 'species'
+    assert tree.common_ancestor(['9606', '10090']).props.get("sci_name") == 'Euarchontoglires'
+
 
-    t2 = ncbi.get_lineage('649756')
-    assert t2 == [1, 131567, 2, 1783272, 1239, 186801, 3085636, 186803, 207244, 649756]