REF: kaiju

qiime2 · Jul 24, 2024 · 9586682 · 9586682
1 parent 6f7cdb8
commit 9586682
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Showing 9 changed files with 22 additions and 18 deletions.
diff --git a/q2_types/__init__.py b/q2_types/__init__.py
@@ -19,6 +19,5 @@
 importlib.import_module('q2_types.metadata')
 importlib.import_module('q2_types.multiplexed_sequences')
 importlib.import_module('q2_types.kraken2')
-importlib.import_module('q2_types.kaiju')
 importlib.import_module('q2_types.reference_db')
 importlib.import_module('q2_types.profile_hmms')
diff --git a/q2_types/kaiju/__init__.py b/q2_types/kaiju/__init__.py
@@ -6,12 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-import importlib
-
-from ._format import KaijuIndexFormat, KaijuDBDirectoryFormat
-from ._type import KaijuDB
+from ._formats import KaijuIndexFormat, KaijuDBDirectoryFormat
+from ._types import KaijuDB
 
 __all__ = ["KaijuIndexFormat", "KaijuDBDirectoryFormat", "KaijuDB"]
-
-importlib.import_module('q2_types.kaiju._format')
-importlib.import_module('q2_types.kaiju._type')
diff --git a/q2_types/kaiju/_type.py → q2_types/kaiju/_deferred_setup/__init__.py b/q2_types/kaiju/_type.py → q2_types/kaiju/_deferred_setup/__init__.py
@@ -5,13 +5,12 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-from qiime2.plugin import SemanticType
 
-from . import KaijuDBDirectoryFormat
-from ..plugin_setup import plugin
+from .. import KaijuIndexFormat, KaijuDBDirectoryFormat, KaijuDB
 
+from ...plugin_setup import plugin
 
-KaijuDB = SemanticType("KaijuDB")
+plugin.register_formats(KaijuDBDirectoryFormat, KaijuIndexFormat)
 
 plugin.register_semantic_types(KaijuDB)
 

diff --git a/q2_types/kaiju/_format.py → q2_types/kaiju/_formats.py b/q2_types/kaiju/_format.py → q2_types/kaiju/_formats.py
@@ -6,10 +6,9 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 from qiime2.plugin import model
-from q2_types.reference_db._format import (
+from q2_types.reference_db import (
     NCBITaxonomyNamesFormat, NCBITaxonomyNodesFormat
 )
-from ..plugin_setup import plugin
 
 
 class KaijuIndexFormat(model.BinaryFileFormat):
@@ -24,6 +23,3 @@ class KaijuDBDirectoryFormat(model.DirectoryFormat):
     nodes = model.File(r"nodes.dmp", format=NCBITaxonomyNodesFormat)
     names = model.File(r"names.dmp", format=NCBITaxonomyNamesFormat)
     index = model.File(r"kaiju_db.+\.fmi", format=KaijuIndexFormat)
-
-
-plugin.register_formats(KaijuDBDirectoryFormat)
diff --git a/q2_types/kaiju/_types.py b/q2_types/kaiju/_types.py
@@ -0,0 +1,11 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+from qiime2.plugin import SemanticType
+
+
+KaijuDB = SemanticType("KaijuDB")
diff --git a/q2_types/kaiju/tests/test_format.py → q2_types/kaiju/tests/test_formats.py b/q2_types/kaiju/tests/test_format.py → q2_types/kaiju/tests/test_formats.py
@@ -8,7 +8,7 @@
 import unittest
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_types.kaiju._format import KaijuDBDirectoryFormat
+from q2_types.kaiju import KaijuDBDirectoryFormat
 
 
 class TestFormats(TestPluginBase):

diff --git a/q2_types/kaiju/tests/test_type.py → q2_types/kaiju/tests/test_types.py b/q2_types/kaiju/tests/test_type.py → q2_types/kaiju/tests/test_types.py
diff --git a/q2_types/plugin_setup.py b/q2_types/plugin_setup.py
@@ -35,5 +35,6 @@
 importlib.import_module('q2_types.feature_map._deferred_setup')
 importlib.import_module('q2_types.feature_table._deferred_setup')
 importlib.import_module('q2_types.genome_data._deferred_setup')
+importlib.import_module('q2_types.kaiju._deferred_setup')
 
 importlib.import_module('q2_types.per_sample_sequences._deferred_setup')
diff --git a/q2_types/reference_db/__init__.py b/q2_types/reference_db/__init__.py
@@ -20,12 +20,15 @@
     DiamondDatabaseFileFmt,
     DiamondDatabaseDirFmt,
     NCBITaxonomyDirFmt,
+    NCBITaxonomyNamesFormat,
+    NCBITaxonomyNodesFormat,
     EggnogProteinSequencesDirFmt
 )
 
 __all__ = ['ReferenceDB', 'Diamond', 'Eggnog', 'DiamondDatabaseFileFmt',
            'DiamondDatabaseDirFmt', 'EggnogRefDirFmt', 'EggnogRefTextFileFmt',
            'EggnogRefBinFileFmt', 'NCBITaxonomyDirFmt', 'NCBITaxonomy',
+           'NCBITaxonomyNamesFormat', 'NCBITaxonomyNodesFormat',
            'EggnogProteinSequencesDirFmt', 'EggnogProteinSequences']
 
 importlib.import_module('q2_types.reference_db._format')