removed nested structure of annotaion type

bokulich-lab · Jul 5, 2024 · 34a34b8 · 34a34b8
1 parent 78c4329
commit 34a34b8
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Showing 4 changed files with 7 additions and 50 deletions.
diff --git a/q2_amr/amrfinderplus/types/_format.py b/q2_amr/amrfinderplus/types/_format.py
@@ -5,8 +5,6 @@
 #
 # 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
@@ -116,22 +114,13 @@ def _validate_(self, level):
 
 
 class ARMFinderPlusAnnotationsDirFmt(MultiDirValidationMixin, model.DirectoryFormat):
-    annotation = model.FileCollection(r".+\.tsv$", format=ARMFinderPlusAnnotationFormat)
+    annotation = model.FileCollection(
+        r".+_amr_(annotations|mutations)\.tsv$", format=ARMFinderPlusAnnotationFormat
+    )
 
     @annotation.set_path_maker
     def annotation_path_maker(self, sample_id, mag_id):
-        return rf"{sample_id}/{mag_id}/.+\.tsv"
-
-    def sample_dict(self):
-        sample_dict = {}
-        for sample in self.path.iterdir():
-            mag_dict = {}
-            for mag in sample.iterdir():
-                mag_dict[mag.name] = [
-                    os.path.join(mag, "amr_annotation.tsv"),
-                ]
-            sample_dict[sample.name] = mag_dict
-        return sample_dict
+        return rf"{sample_id}/{mag_id}_amr_(annotations|mutations)\.tsv$"
 
 
 ARMFinderPlusAnnotationDirFmt = model.SingleFileDirectoryFormat(

diff --git a/...4de3-a957-7e8bf837f30d/amr_annotation.tsv → ...de3-a957-7e8bf837f30d_amr_annotations.tsv b/...4de3-a957-7e8bf837f30d/amr_annotation.tsv → ...de3-a957-7e8bf837f30d_amr_annotations.tsv
diff --git a/...4c4a-a53b-4df6999815dd/amr_annotation.tsv → ...c4a-a53b-4df6999815dd_amr_annotations.tsv b/...4c4a-a53b-4df6999815dd/amr_annotation.tsv → ...c4a-a53b-4df6999815dd_amr_annotations.tsv
diff --git a/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py b/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py
@@ -5,8 +5,6 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-import os
-
 from qiime2.core.exceptions import ValidationError
 from qiime2.plugin.testing import TestPluginBase
 
@@ -27,8 +25,8 @@ def test_amrfinderplus_database_directory_format_validate_positive(self):
 
     def test_amrfinderplus_annotation_format_validate_positive(self):
         filepath = self.get_data_path(
-            "annotation/no_coordinates/aa447c99-ecd9-4c4a-a53b-4df6999815dd"
-            "/amr_annotation.tsv"
+            "annotation/no_coordinates/"
+            "aa447c99-ecd9-4c4a-a53b-4df6999815dd_amr_annotations.tsv"
         )
 
         format = ARMFinderPlusAnnotationFormat(filepath, mode="r")
@@ -37,7 +35,7 @@ def test_amrfinderplus_annotation_format_validate_positive(self):
     def test_amrfinderplus_annotation_format_validate_positive_coordinates(self):
         filepath = self.get_data_path(
             "annotation/coordinates/e026af61-d911-4de3-a957-7e8bf837f30d"
-            "/amr_annotation.tsv"
+            "_amr_annotations.tsv"
         )
         format = ARMFinderPlusAnnotationFormat(filepath, mode="r")
         format.validate()
@@ -83,36 +81,6 @@ def test_amrfinderplus_annotation_format_validation_error(self):
 
             self.assertEqual(str(context.exception), expected_message)
 
-    def test_amrfinderplus_annotations_directory_format_sample_dict(self):
-        dirpath = self.get_data_path("annotation")
-        annotations = ARMFinderPlusAnnotationsDirFmt(dirpath, mode="r")
-
-        obs = annotations.sample_dict()
-
-        exp = {
-            "coordinates": {
-                "e026af61-d911-4de3-a957-7e8bf837f30d": [
-                    os.path.join(
-                        annotations.path,
-                        "coordinates",
-                        "e026af61-d911-4de3-a957-7e8bf837f30d",
-                        "amr_annotation.tsv",
-                    ),
-                ]
-            },
-            "no_coordinates": {
-                "aa447c99-ecd9-4c4a-a53b-4df6999815dd": [
-                    os.path.join(
-                        annotations.path,
-                        "no_coordinates",
-                        "aa447c99-ecd9-4c4a-a53b-4df6999815dd",
-                        "amr_annotation.tsv",
-                    ),
-                ],
-            },
-        }
-        self.assertEqual(obs, exp)
-
     def test_amrfinderplus_annotation_directory_format(self):
         dirpath = self.get_data_path(
             "annotation/coordinates/e026af61-d911-4de3-a957-7e8bf837f30d"