chnages in annotation action

q2_amr/amrfinderplus/sample_data.py

@@ -32,9 +32,9 @@ def annotate_sample_data_amrfinderplus(
     GenesDirectoryFormat,
     pd.DataFrame,
 ):
-    annotations = AMRFinderPlusAnnotationsDirFmt()
-    mutations = AMRFinderPlusAnnotationsDirFmt()
-    genes = GenesDirectoryFormat()
+    amr_annotations = AMRFinderPlusAnnotationsDirFmt()
+    amr_all_mutations = AMRFinderPlusAnnotationsDirFmt()
+    amr_genes = GenesDirectoryFormat()
     frequency_list = []
 
     # Create list of paths to all mags or contigs
@@ -86,20 +86,22 @@ def annotate_sample_data_amrfinderplus(
 
             # Move mutations file. If it is not created, create an empty mutations file
             des_path_mutations = os.path.join(
-                str(mutations),
+                str(amr_all_mutations),
                 sample_id,
-                f"{mag_id + '_' if mag_id else ''}amr_mutations.tsv",
+                f"{mag_id + '_' if mag_id else ''}amr_all_mutations.tsv",
             )
             os.makedirs(os.path.dirname(des_path_mutations), exist_ok=True)
             if organism:
-                shutil.move(os.path.join(tmp, "amr_mutations.tsv"), des_path_mutations)
+                shutil.move(
+                    os.path.join(tmp, "amr_all_mutations.tsv"), des_path_mutations
+                )
             else:
                 with open(des_path_mutations, "w"):
                     pass
 
             # Move annotations file
             des_path_annotations = os.path.join(
-                str(annotations),
+                str(amr_annotations),
                 sample_id,
                 f"{mag_id + '_' if mag_id else ''}amr_annotations.tsv",
             )
@@ -110,14 +112,14 @@ def annotate_sample_data_amrfinderplus(
             shutil.move(
                 os.path.join(tmp, "amr_genes.fasta"),
                 os.path.join(
-                    str(genes), f"{mag_id if mag_id else sample_id}_amr_genes.fasta"
+                    str(amr_genes), f"{mag_id if mag_id else sample_id}_amr_genes.fasta"
                 ),
             )
 
         feature_table = create_count_table(df_list=frequency_list)
     return (
-        annotations,
-        mutations,
-        genes,
+        amr_annotations,
+        amr_all_mutations,
+        amr_genes,
         feature_table,
     )

q2_amr/amrfinderplus/tests/test_sample_data.py

@@ -30,21 +30,21 @@ def mock_run_amrfinderplus_n(
         with open(os.path.join(working_dir, "amr_annotations.tsv"), "w"):
             pass
         if organism:
-            with open(os.path.join(working_dir, "amr_mutations.tsv"), "w"):
+            with open(os.path.join(working_dir, "amr_all_mutations.tsv"), "w"):
                 pass
         if dna_sequences:
             with open(os.path.join(working_dir, "amr_genes.fasta"), "w"):
                 pass
 
     files_contigs = [
         "amr_annotations.tsv",
-        "amr_mutations.tsv",
+        "amr_all_mutations.tsv",
         "sample1_amr_genes.fasta",
     ]
 
     files_mags = [
         "mag1_amr_annotations.tsv",
-        "mag1_amr_mutations.tsv",
+        "mag1_amr_all_mutations.tsv",
         "mag1_amr_genes.fasta",
     ]
 

q2_amr/amrfinderplus/tests/test_utils.py

@@ -48,7 +48,7 @@ def test_run_amrfinderplus_n(self, mock_run_command):
                 "--organism",
                 "Escherichia",
                 "--mutation_all",
-                "path_dir/amr_mutations.tsv",
+                "path_dir/amr_all_mutations.tsv",
                 "--plus",
                 "--report_all_equal",
                 "--ident_min",

q2_amr/amrfinderplus/utils.py

@@ -57,7 +57,7 @@ def run_amrfinderplus_n(
                 "--organism",
                 organism,
                 "--mutation_all",
-                f"{working_dir}/amr_mutations.tsv",
+                f"{working_dir}/amr_all_mutations.tsv",
             ]
         )
     if plus:

q2_amr/plugin_setup.py

@@ -1173,9 +1173,9 @@
         "threads": Int % Range(0, None, inclusive_start=False),
     },
     outputs=[
-        ("annotations", SampleData[AMRFinderPlusAnnotations]),
-        ("mutations", SampleData[AMRFinderPlusAnnotations]),
-        ("genes", GenomeData[Genes]),
+        ("amr_annotations", SampleData[AMRFinderPlusAnnotations]),
+        ("amr_all_mutations", SampleData[AMRFinderPlusAnnotations]),
+        ("amr_genes", GenomeData[Genes]),
         ("feature_table", FeatureTable[Frequency]),
     ],
     input_descriptions={
@@ -1210,8 +1210,8 @@
         "fail. Using more than 4 threads may speed up searches.",
     },
     output_descriptions={
-        "annotations": "Annotated AMR genes and mutations.",
-        "mutations": "Report of genotypes at all locations screened for point "
+        "amr_annotations": "Annotated AMR genes and mutations.",
+        "amr_all_mutations": "Report of genotypes at all locations screened for point "
         "mutations. These files allow you to distinguish between called "
         "point mutations that were the sensitive variant and the point "
         "mutations that could not be called because the sequence was not "
@@ -1224,8 +1224,8 @@
         "'Gene symbols' from known point-mutation sites have gene symbols "
         "that match the Pathogen Detection Reference Gene Catalog "
         "standardized nomenclature for point mutations.",
-        "genes": "Sequences that were identified by AMRFinderPlus as AMR genes. This "
-        "will include the entire region that aligns to the references for "
+        "amr_genes": "Sequences that were identified by AMRFinderPlus as AMR genes. "
+        "This will include the entire region that aligns to the references for "
         "point mutations.",
         "feature_table": "Presence/Absence table of ARGs in all samples.",
     },