dirformat with filecollections

q2_amr/amrfinderplus/types/__init__.py

@@ -5,5 +5,14 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+from q2_amr.amrfinderplus.types._format import (
+    AMRFinderPlusDatabaseDirectoryFormat,
+    BinaryFormat,
+    TextFormat,
+)
 
-__all__ = []
+__all__ = [
+    "AMRFinderPlusDatabaseDirectoryFormat",
+    "TextFormat",
+    "BinaryFormat",
+]

q2_amr/amrfinderplus/types/_format.py

@@ -5,3 +5,38 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+from q2_types.feature_data import MixedCaseDNAFASTAFormat, ProteinFASTAFormat
+from qiime2.plugin import model
+
+
+class TextFormat(model.TextFileFormat):
+    def _validate_(self, level):
+        pass
+
+
+class BinaryFormat(model.BinaryFileFormat):
+    def _validate_(self, level):
+        pass
+
+
+class AMRFinderPlusDatabaseDirectoryFormat(model.DirectoryFormat):
+    AMR_LIB = model.File("AMR.LIB", format=TextFormat)
+    AMR_LIB_comp = model.FileCollection(r"AMR\.LIB\.h3.$", format=BinaryFormat)
+    AMRProt = model.File("AMRProt", format=ProteinFASTAFormat)
+    AMRProt_blast = model.FileCollection(r"AMRProt\.p..$", format=BinaryFormat)
+    AMRProt_mutation = model.File("AMRProt-mutation.tab", format=TextFormat)
+    AMRProt_suppress = model.File("AMRProt-suppress", format=TextFormat)
+    AMRProt_susceptible = model.File("AMRProt-susceptible.tab", format=TextFormat)
+    changes = model.File("changes.txt", format=TextFormat)
+    db_version = model.File("database_format_version.txt", format=TextFormat)
+    fam = model.File("fam.tab", format=TextFormat)
+    taxgroup = model.File("taxgroup.tab", format=TextFormat)
+    version = model.File("version.txt", format=TextFormat)
+    AMR_DNA = model.FileCollection(
+        r"^AMR_DNA-[a-zA-Z_]+$", format=MixedCaseDNAFASTAFormat
+    )
+    AMR_DNA_comp = model.FileCollection(
+        r"^AMR_DNA-[a-zA-Z_]+\.n..$", format=BinaryFormat
+    )
+    AMR_CDS_comp = model.FileCollection(r"^AMR_CDS\.n..$", format=BinaryFormat)
+    AMR_CDS = model.File("AMR_CDS", format=MixedCaseDNAFASTAFormat)

q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py

@@ -5,3 +5,16 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+from qiime2.plugin.testing import TestPluginBase
+
+from q2_amr.amrfinderplus.types._format import AMRFinderPlusDatabaseDirectoryFormat
+
+
+class TestAMRFinderPlusDatabaseTypesAndFormats(TestPluginBase):
+    package = "q2_amr.amrfinderplus.types.tests"
+
+    def test_amrfinderplus_database_directory_format_validate_positive(self):
+        format = AMRFinderPlusDatabaseDirectoryFormat(
+            "/Users/rischv/Documents/data/amrfinder/database", mode="r"
+        )
+        format.validate()

q2_amr/plugin_setup.py

@@ -28,6 +28,12 @@
 from qiime2.plugin import Citations, Plugin
 
 from q2_amr import __version__
+from q2_amr.amrfinderplus.types._format import (
+    AMRFinderPlusDatabaseDirectoryFormat,
+    BinaryFormat,
+    TextFormat,
+)
+from q2_amr.amrfinderplus.types._type import AMRFinderPlusDatabase
 from q2_amr.card.database import fetch_card_db
 from q2_amr.card.heatmap import heatmap
 from q2_amr.card.mags import annotate_mags_card
@@ -468,6 +474,7 @@
     CARDReadsGeneKmerAnalysis,
     CARDReadsAlleleKmerAnalysis,
     CARDMAGsKmerAnalysis,
+    AMRFinderPlusDatabase,
 )
 
 plugin.register_semantic_type_to_format(
@@ -498,6 +505,10 @@
     SampleData[CARDMAGsKmerAnalysis],
     artifact_format=CARDMAGsKmerAnalysisDirectoryFormat,
 )
+plugin.register_semantic_type_to_format(
+    AMRFinderPlusDatabase,
+    artifact_format=AMRFinderPlusDatabaseDirectoryFormat,
+)
 plugin.register_formats(
     CARDKmerDatabaseDirectoryFormat,
     CARDKmerJSONFormat,
@@ -522,6 +533,9 @@
     CARDReadsKmerAnalysisJSONFormat,
     CARDReadsGeneKmerAnalysisDirectoryFormat,
     CARDReadsAlleleKmerAnalysisDirectoryFormat,
+    AMRFinderPlusDatabaseDirectoryFormat,
+    TextFormat,
+    BinaryFormat,
 )
 
 importlib.import_module("q2_amr.card.types._transformer")