Revert "ENH: Removed AMRFinderPlusAnnotation type (bokulich-lab#95)"

This reverts commit b661340.

q2_amr/amrfinderplus/sample_data.py

@@ -32,9 +32,9 @@ def annotate_sample_data_amrfinderplus(
     GenesDirectoryFormat,
     pd.DataFrame,
 ):
-    amr_annotations = AMRFinderPlusAnnotationsDirFmt()
-    amr_all_mutations = AMRFinderPlusAnnotationsDirFmt()
-    amr_genes = GenesDirectoryFormat()
+    annotations = AMRFinderPlusAnnotationsDirFmt()
+    mutations = AMRFinderPlusAnnotationsDirFmt()
+    genes = GenesDirectoryFormat()
     frequency_list = []
 
     # Create list of paths to all mags or contigs
@@ -86,22 +86,20 @@ 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(amr_all_mutations),
+                str(mutations),
                 sample_id,
-                f"{mag_id + '_' if mag_id else ''}amr_all_mutations.tsv",
+                f"{mag_id + '_' if mag_id else ''}amr_mutations.tsv",
             )
             os.makedirs(os.path.dirname(des_path_mutations), exist_ok=True)
             if organism:
-                shutil.move(
-                    os.path.join(tmp, "amr_all_mutations.tsv"), des_path_mutations
-                )
+                shutil.move(os.path.join(tmp, "amr_mutations.tsv"), des_path_mutations)
             else:
                 with open(des_path_mutations, "w"):
                     pass
 
             # Move annotations file
             des_path_annotations = os.path.join(
-                str(amr_annotations),
+                str(annotations),
                 sample_id,
                 f"{mag_id + '_' if mag_id else ''}amr_annotations.tsv",
             )
@@ -112,14 +110,14 @@ def annotate_sample_data_amrfinderplus(
             shutil.move(
                 os.path.join(tmp, "amr_genes.fasta"),
                 os.path.join(
-                    str(amr_genes), f"{mag_id if mag_id else sample_id}_amr_genes.fasta"
+                    str(genes), f"{mag_id if mag_id else sample_id}_amr_genes.fasta"
                 ),
             )
 
         feature_table = create_count_table(df_list=frequency_list)
     return (
-        amr_annotations,
-        amr_all_mutations,
-        amr_genes,
+        annotations,
+        mutations,
+        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_all_mutations.tsv"), "w"):
+            with open(os.path.join(working_dir, "amr_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_all_mutations.tsv",
+        "amr_mutations.tsv",
         "sample1_amr_genes.fasta",
     ]
 
     files_mags = [
         "mag1_amr_annotations.tsv",
-        "mag1_amr_all_mutations.tsv",
+        "mag1_amr_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_all_mutations.tsv",
+                "path_dir/amr_mutations.tsv",
                 "--plus",
                 "--report_all_equal",
                 "--ident_min",

q2_amr/amrfinderplus/types/__init__.py

@@ -6,6 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 from q2_amr.amrfinderplus.types._format import (
+    AMRFinderPlusAnnotationDirFmt,
     AMRFinderPlusAnnotationFormat,
     AMRFinderPlusAnnotationsDirFmt,
     AMRFinderPlusDatabaseDirFmt,
@@ -17,6 +18,7 @@
     "AMRFinderPlusDatabaseDirFmt",
     "AMRFinderPlusAnnotationFormat",
     "AMRFinderPlusAnnotationsDirFmt",
+    "AMRFinderPlusAnnotationDirFmt",
     "TextFormat",
     "BinaryFormat",
 ]

q2_amr/amrfinderplus/types/_format.py

@@ -5,10 +5,9 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-import os
-
 import pandas as pd
 from q2_types.feature_data import MixedCaseDNAFASTAFormat, ProteinFASTAFormat
+from q2_types.per_sample_sequences._format import MultiDirValidationMixin
 from qiime2.core.exceptions import ValidationError
 from qiime2.plugin import model
 
@@ -110,11 +109,19 @@ def _validate_(self, level):
         self._validate()
 
 
-class AMRFinderPlusAnnotationsDirFmt(model.DirectoryFormat):
-    annotations = model.FileCollection(
-        r".*amr_(annotations|all_mutations)\.tsv$", format=AMRFinderPlusAnnotationFormat
+class AMRFinderPlusAnnotationsDirFmt(MultiDirValidationMixin, model.DirectoryFormat):
+    annotation = model.FileCollection(
+        r".*amr_(annotations|mutations)\.tsv$", format=AMRFinderPlusAnnotationFormat
     )
 
-    @annotations.set_path_maker
-    def annotations_path_maker(self, name, id, dir_name=""):
-        return os.path.join(dir_name, f"{id}_amr_{name}.tsv")
+    @annotation.set_path_maker
+    def annotation_path_maker(self, sample_id, mag_id):
+        prefix = f"{sample_id}/{mag_id}_" if mag_id else f"{sample_id}/"
+        return f"{prefix}amr_annotations.tsv"
+
+
+AMRFinderPlusAnnotationDirFmt = model.SingleFileDirectoryFormat(
+    "AMRFinderPlusAnnotationDirFmt",
+    r"amr_(annotations|mutations)\.tsv$",
+    AMRFinderPlusAnnotationFormat,
+)

q2_amr/amrfinderplus/types/_type.py

@@ -11,6 +11,8 @@
 
 AMRFinderPlusDatabase = SemanticType("AMRFinderPlusDatabase")
 AMRFinderPlusAnnotations = SemanticType(
-    "AMRFinderPlusAnnotations",
-    variant_of=[SampleData.field["type"], FeatureData.field["type"]],
+    "AMRFinderPlusAnnotations", variant_of=SampleData.field["type"]
+)
+AMRFinderPlusAnnotation = SemanticType(
+    "AMRFinderPlusAnnotation", variant_of=FeatureData.field["type"]
 )

q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py

@@ -12,6 +12,7 @@
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_amr.amrfinderplus.types._format import (
+    AMRFinderPlusAnnotationDirFmt,
     AMRFinderPlusAnnotationFormat,
     AMRFinderPlusAnnotationsDirFmt,
     AMRFinderPlusDatabaseDirFmt,
@@ -91,28 +92,14 @@ def test_amrfinderplus_annotation_format_validation_error(self):
 
             self.assertEqual(str(context.exception), expected_message)
 
-    def test_amrfinderplus_annotations_dir_fmt_feature(self):
+    def test_amrfinderplus_annotation_directory_format(self):
         dirpath = self.get_data_path(
             "annotation/coordinates/e026af61-d911-4de3-a957-7e8bf837f30d"
         )
-        annotations = AMRFinderPlusAnnotationsDirFmt(dirpath, mode="r")
-        assert isinstance(annotations, AMRFinderPlusAnnotationsDirFmt)
+        annotations = AMRFinderPlusAnnotationDirFmt(dirpath, mode="r")
+        assert isinstance(annotations, AMRFinderPlusAnnotationDirFmt)
 
-    def test_amrfinderplus_annotations_dir_fmt_sample(self):
+    def test_amrfinderplus_annotations_directory_format(self):
         dirpath = self.get_data_path("annotation")
         annotations = AMRFinderPlusAnnotationsDirFmt(dirpath, mode="r")
         assert isinstance(annotations, AMRFinderPlusAnnotationsDirFmt)
-
-    def test_amrfinderplus_annotations_dir_fmt_path_maker_dir_name(self):
-        fmt = AMRFinderPlusAnnotationsDirFmt()
-        path = fmt.annotations_path_maker(
-            name="annotations", id="id", dir_name="dir_name"
-        )
-        self.assertEqual(
-            str(path), os.path.join(str(fmt), "dir_name/id_amr_annotations.tsv")
-        )
-
-    def test_amrfinderplus_annotations_dir_fmt_path_maker(self):
-        fmt = AMRFinderPlusAnnotationsDirFmt()
-        path = fmt.annotations_path_maker(name="annotations", id="id")
-        self.assertEqual(str(path), os.path.join(str(fmt), "id_amr_annotations.tsv"))

q2_amr/amrfinderplus/utils.py

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

q2_amr/plugin_setup.py

@@ -35,13 +35,15 @@
 from q2_amr.amrfinderplus.database import fetch_amrfinderplus_db
 from q2_amr.amrfinderplus.sample_data import annotate_sample_data_amrfinderplus
 from q2_amr.amrfinderplus.types._format import (
+    AMRFinderPlusAnnotationDirFmt,
     AMRFinderPlusAnnotationFormat,
     AMRFinderPlusAnnotationsDirFmt,
     AMRFinderPlusDatabaseDirFmt,
     BinaryFormat,
     TextFormat,
 )
 from q2_amr.amrfinderplus.types._type import (
+    AMRFinderPlusAnnotation,
     AMRFinderPlusAnnotations,
     AMRFinderPlusDatabase,
 )
@@ -1173,9 +1175,9 @@
         "threads": Int % Range(0, None, inclusive_start=False),
     },
     outputs=[
-        ("amr_annotations", SampleData[AMRFinderPlusAnnotations]),
-        ("amr_all_mutations", SampleData[AMRFinderPlusAnnotations]),
-        ("amr_genes", GenomeData[Genes]),
+        ("annotations", SampleData[AMRFinderPlusAnnotations]),
+        ("mutations", SampleData[AMRFinderPlusAnnotations]),
+        ("genes", GenomeData[Genes]),
         ("feature_table", FeatureTable[Frequency]),
     ],
     input_descriptions={
@@ -1210,8 +1212,8 @@
         "fail. Using more than 4 threads may speed up searches.",
     },
     output_descriptions={
-        "amr_annotations": "Annotated AMR genes and mutations.",
-        "amr_all_mutations": "Report of genotypes at all locations screened for point "
+        "annotations": "Annotated AMR genes and mutations.",
+        "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 +1226,8 @@
         "'Gene symbols' from known point-mutation sites have gene symbols "
         "that match the Pathogen Detection Reference Gene Catalog "
         "standardized nomenclature for point mutations.",
-        "amr_genes": "Sequences that were identified by AMRFinderPlus as AMR genes. "
-        "This will include the entire region that aligns to the references for "
+        "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.",
     },
@@ -1247,6 +1249,7 @@
     CARDMAGsKmerAnalysis,
     AMRFinderPlusDatabase,
     AMRFinderPlusAnnotations,
+    AMRFinderPlusAnnotation,
 )
 
 plugin.register_semantic_type_to_format(
@@ -1286,8 +1289,8 @@
     artifact_format=AMRFinderPlusAnnotationsDirFmt,
 )
 plugin.register_semantic_type_to_format(
-    FeatureData[AMRFinderPlusAnnotations],
-    artifact_format=AMRFinderPlusAnnotationsDirFmt,
+    FeatureData[AMRFinderPlusAnnotation],
+    artifact_format=AMRFinderPlusAnnotationDirFmt,
 )
 plugin.register_formats(
     CARDKmerDatabaseDirectoryFormat,
@@ -1318,6 +1321,7 @@
     BinaryFormat,
     AMRFinderPlusAnnotationFormat,
     AMRFinderPlusAnnotationsDirFmt,
+    AMRFinderPlusAnnotationDirFmt,
 )
 
 importlib.import_module("q2_amr.card.types._transformer")