3 changes after comments from michal

q2_amr/plugin_setup.py

@@ -162,10 +162,10 @@
     output_descriptions={
         "amr_allele_annotation": "AMR annotation mapped on alleles.",
         "amr_gene_annotation": "AMR annotation mapped on genes.",
-        "allele_feature_table": "Presence and absence table of ARGs in all samples for"
-        " allele mapping.",
-        "gene_feature_table": "Presence and absence table of ARGs in all samples for "
-        "gene mapping.",
+        "allele_feature_table": "Frequency table of ARGs in all samples for allele "
+        "mapping.",
+        "gene_feature_table": "Frequency table of ARGs in all samples for gene "
+        "mapping.",
     },
     name="Annotate reads with antimicrobial resistance genes from CARD.",
     description="Annotate reads with antimicrobial resistance genes from CARD.",

q2_amr/tests/card/test_utils.py

@@ -39,6 +39,7 @@ def setUpClass(cls):
                 "mdtE": ["0", "1"],
             }
         )
+        cls.frequency_table.set_index("sample_id", inplace=True)
 
     def test_load_card_db_fasta(self):
         # Create CARD and Kmer database objects
@@ -122,13 +123,13 @@ def test_exception_raised(self):
             self.assertEqual(str(cm.exception), expected_message)
 
     def test_read_in_txt_mags(self):
-        # Test read_read_in_txt with output data from annotate_mags_card
+        # Test read_in_txt with output data from annotate_mags_card
         self.read_in_txt_test_body(
             "output.mags.txt", "sample1", self.count_df_list[2], "mags"
         )
 
     def test_read_in_txt_reads(self):
-        # Test read_read_in_txt with output data from annotate_reads_card
+        # Test read_in_txt with output data from annotate_reads_card
         self.read_in_txt_test_body(
             "output.allele_mapping_data.txt", "sample1", self.count_df_list[0], "reads"
         )
@@ -145,9 +146,8 @@ def test_create_count_table(self):
         obs = create_count_table(df_list)
         obs = obs.astype(str)
 
-        # Create expected count table from
+        # Define expected count table
         exp = self.frequency_table
-        exp.set_index("sample_id", inplace=True)
 
         # Compare expected and observed count table
         pd.testing.assert_frame_equal(exp, obs)