ENH: add FeatureData[Contig] type (#314)

qiime2 · Mar 13, 2024 · f5bce08 · f5bce08
1 parent b21fb99
commit f5bce08
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Showing 3 changed files with 24 additions and 4 deletions.
diff --git a/q2_types/feature_data_mag/__init__.py b/q2_types/feature_data_mag/__init__.py
@@ -14,12 +14,12 @@
         OrthologFileFmt
         )
 
-from ._type import MAG, NOG, OG, KEGG
+from ._type import MAG, NOG, OG, KEGG, Contig
 from ._transformer import MAGIterator
 
 __all__ = [
         'MAG', 'MAGSequencesDirFmt', 'MAGIterator', 'NOG', 'OG', 'KEGG',
-        'OrthologAnnotationDirFmt', 'OrthologFileFmt',
+        'OrthologAnnotationDirFmt', 'OrthologFileFmt', 'Contig'
         ]
 
 importlib.import_module('q2_types.feature_data._format')

diff --git a/q2_types/feature_data_mag/_type.py b/q2_types/feature_data_mag/_type.py
@@ -13,6 +13,7 @@
         )
 from qiime2.core.type import SemanticType
 
+from ..per_sample_sequences import ContigSequencesDirFmt
 from ..plugin_setup import plugin
 
 
@@ -24,6 +25,14 @@
     artifact_format=MAGSequencesDirFmt
 )
 
+Contig = SemanticType('Contig', variant_of=FeatureData.field['type'])
+
+plugin.register_semantic_types(Contig)
+plugin.register_semantic_type_to_format(
+    FeatureData[Contig],
+    artifact_format=ContigSequencesDirFmt
+)
+
 NOG = SemanticType('NOG', variant_of=FeatureData.field['type'])
 
 plugin.register_semantic_types(NOG)

diff --git a/q2_types/feature_data_mag/tests/test_type.py b/q2_types/feature_data_mag/tests/test_type.py
@@ -12,8 +12,10 @@
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_types.feature_data_mag import (
-        MAG, MAGSequencesDirFmt, OrthologAnnotationDirFmt, NOG, OG, KEGG,
-        )
+        MAG, MAGSequencesDirFmt, OrthologAnnotationDirFmt,
+        NOG, OG, KEGG, Contig
+)
+from q2_types.per_sample_sequences import ContigSequencesDirFmt
 
 
 class TestTypes(TestPluginBase):
@@ -28,6 +30,15 @@ def test_mags_semantic_type_to_format_registration(self):
             MAGSequencesDirFmt
         )
 
+    def test_contig_semantic_type_registration(self):
+        self.assertRegisteredSemanticType(Contig)
+
+    def test_contig_semantic_type_to_format_registration(self):
+        self.assertSemanticTypeRegisteredToFormat(
+            FeatureData[Contig],
+            ContigSequencesDirFmt
+        )
+
     def test_nog_type_registration(self):
         self.assertRegisteredSemanticType(NOG)