fix by filtering nan's in test

galaxyproteomics · Apr 19, 2019 · 07004a0 · 07004a0
1 parent 5134acb
commit 07004a0
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/tests/travis/testNCBITaxonomyDb.py b/tests/travis/testNCBITaxonomyDb.py
@@ -23,7 +23,9 @@ def testMapIdToDesiredRanks_Unipept(self):
         # not contained in FULL_TAXONOMY_TREE
         tax = testfile('unipept_sample7_taxonomy.tab')
         df = pd.read_csv(tax, sep='\t')
-        num_ids = self.ncbi.convert_name_to_taxid(df['lca'])
+        num_ids = np.array(self.ncbi.convert_name_to_taxid(df['lca']))
+        # filter out nans - this happens in the code
+        num_ids = num_ids[~np.isnan(num_ids)]
         for i in num_ids:
             self.ncbi.map_id_to_desired_ranks(td.BASIC_TAXONOMY_TREE, i)