diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py index 68228a1..413e850 100644 --- a/q2_amr/plugin_setup.py +++ b/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.", diff --git a/q2_amr/tests/card/test_utils.py b/q2_amr/tests/card/test_utils.py index 1e04042..a68008b 100644 --- a/q2_amr/tests/card/test_utils.py +++ b/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)