required updates to FeatureData[MAG]

misialq · Jul 11, 2023 · a632195 · a632195
1 parent 5737261
commit a632195
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Showing 7 changed files with 32 additions and 28 deletions.
diff --git a/q2_types_genomics/feature_data/_format.py b/q2_types_genomics/feature_data/_format.py
@@ -14,24 +14,24 @@
 
 
 MAGSequencesDirFmt = model.SingleFileDirectoryFormat(
-    'MAGSequencesDirFmt', r'mag[0-9]+\.(fa|fasta)$', DNAFASTAFormat)
-
-plugin.register_formats(
-    MAGSequencesDirFmt
+    "MAGSequencesDirFmt",
+    r"^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-"
+    r"[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$",
+    DNAFASTAFormat,
 )
 
+plugin.register_formats(MAGSequencesDirFmt)
+
 
 class OrthologAnnotationDirFmt(model.DirectoryFormat):
     annotations = model.FileCollection(
-            r'.+\.annotations',
-            format=OrthologFileFmt
-            )
+        r'.+\.annotations',
+        format=OrthologFileFmt
+    )
 
     @annotations.set_path_maker
     def annotations_path_maker(self, file_name):
         return file_name.split(sep="_")[0]
 
 
-plugin.register_formats(
-        OrthologAnnotationDirFmt
-        )
+plugin.register_formats(OrthologAnnotationDirFmt)
diff --git a/...s/feature_data/tests/data/mags-fa/mag1.fa → ...a/23c5b64e-3f3e-4688-9862-e9dae4fa0f5b.fa b/...s/feature_data/tests/data/mags-fa/mag1.fa → ...a/23c5b64e-3f3e-4688-9862-e9dae4fa0f5b.fa
diff --git a/...s/feature_data/tests/data/mags-fa/mag2.fa → ...a/70c5a728-96a6-4eed-b9f9-9a73153c1385.fa b/...s/feature_data/tests/data/mags-fa/mag2.fa → ...a/70c5a728-96a6-4eed-b9f9-9a73153c1385.fa
diff --git a/...s/feature_data/tests/data/mags-fa/mag3.fa → ...a/7e2a749a-a19a-4b62-8195-0ee601b5fdfb.fa b/...s/feature_data/tests/data/mags-fa/mag3.fa → ...a/7e2a749a-a19a-4b62-8195-0ee601b5fdfb.fa
diff --git a/...ure_data/tests/data/mags-fasta/mag2.fasta → ...b7d53fb-5b60-46c6-8819-aeda065b12e9.fasta b/...ure_data/tests/data/mags-fasta/mag2.fasta → ...b7d53fb-5b60-46c6-8819-aeda065b12e9.fasta
diff --git a/...ure_data/tests/data/mags-fasta/mag1.fasta → ...232c7e1-8ed7-47c8-9bdb-b94706a26931.fasta b/...ure_data/tests/data/mags-fasta/mag1.fasta → ...232c7e1-8ed7-47c8-9bdb-b94706a26931.fasta
diff --git a/q2_types_genomics/feature_data/tests/test_transformers.py b/q2_types_genomics/feature_data/tests/test_transformers.py
@@ -27,23 +27,27 @@ class TestTransformers(TestPluginBase):
     def setUp(self):
         super().setUp()
         self.mags_fa = {
-            'mag1': {
+            '23c5b64e-3f3e-4688-9862-e9dae4fa0f5b': {
                 'k129_5480': 'TTATTTTCAAGATAATGAGCCAATTTAAGCGGTGTCTGGCCG'
                              'CCAAGCTGCACGATCACACCTTTAA'
             },
-            'mag2': {
+            '70c5a728-96a6-4eed-b9f9-9a73153c1385': {
                 'k129_5112': 'CCCCGGAAAGGGCTGGCGACCGACGATGACCTCGGGAAGCCC'
                              'CAACTCGCGGCCGATGGCGCGTACCTCGTC'
             },
-            'mag3': {
+            '7e2a749a-a19a-4b62-8195-0ee601b5fdfb': {
                 'k129_6525': 'AAACTCTATCAAGCGTATACCAAAGTGAGTGGTGTATTGATC'
                              'AGTCAGCTCATTATTGAATCGGA',
                 'k129_6531': 'TCGGATTTGCCGAATGCTTTTTGTAAGGGCCTTCAATTGATT'
                              'TGGCGATAGCGAGCCCGTATTTACGGT'
             }
         }
         self.mags_fasta = {
-            'mag1': {
+            '3b7d53fb-5b60-46c6-8819-aeda065b12e9': {
+                'k129_5401': 'CCATTGTATGTCTTTAGGTAGCTCCTCATGTTTGAGGTTCAT'
+                             'GTCTTGGATTTTGTTTTCTCCAAAAATC'
+            },
+            '6232c7e1-8ed7-47c8-9bdb-b94706a26931': {
                 'k129_4684': 'TGATACCGACGCGGCACTTGAGTGCGCGCTATCCTTCAAGGA'
                              'AGCCACATGCGTTATTGTTAAACA',
                 'k129_5618': 'GTGCTAATCGCACCCTCATGAGCGACACCATTATTCTTTATT'
@@ -53,10 +57,6 @@ def setUp(self):
                 'k129_2817': 'GTCGCCAATTAGCAACTATGATGTCTTCTGGAGTACCTTTGG'
                              'TCCAATCATTTGAAATCA'
             },
-            'mag2': {
-                'k129_5401': 'CCATTGTATGTCTTTAGGTAGCTCCTCATGTTTGAGGTTCAT'
-                             'GTCTTGGATTTTGTTTTCTCCAAAAATC'
-            }
         }
 
     @staticmethod
@@ -86,11 +86,13 @@ def read_seqs_into_dict(loc):
         return seqs
 
     def test_mag_sequences_dir_fmt_to_dataframe(self):
-        _, obs = self.transform_format(MAGSequencesDirFmt, pd.DataFrame,
-                                       filenames=[
-                                           'mags-fasta/mag1.fasta',
-                                           'mags-fasta/mag2.fasta',
-                                       ])
+        _, obs = self.transform_format(
+            MAGSequencesDirFmt, pd.DataFrame,
+            filenames=[
+               'mags-fasta/3b7d53fb-5b60-46c6-8819-aeda065b12e9.fasta',
+               'mags-fasta/6232c7e1-8ed7-47c8-9bdb-b94706a26931.fasta',
+            ]
+        )
         exp = self.mags_to_df(self.mags_fasta)
         pd.testing.assert_frame_equal(exp, obs)
 
@@ -105,11 +107,13 @@ def test_dataframe_to_mag_sequences_dir_fmt(self):
         self.assertDictEqual(self.mags_fasta, obs_seqs)
 
     def test_mag_sequences_dir_fmt_to_mag_iterator(self):
-        _, obs = self.transform_format(MAGSequencesDirFmt, MAGIterator,
-                                       filenames=[
-                                           'mags-fasta/mag1.fasta',
-                                           'mags-fasta/mag2.fasta',
-                                       ])
+        _, obs = self.transform_format(
+            MAGSequencesDirFmt, MAGIterator,
+            filenames=[
+               'mags-fasta/6232c7e1-8ed7-47c8-9bdb-b94706a26931.fasta',
+               'mags-fasta/3b7d53fb-5b60-46c6-8819-aeda065b12e9.fasta',
+            ]
+        )
 
         exp = self.create_multi_generator(self.mags_fasta)
         for e, o in zip(exp, obs):