added collate_ortholog_annotations from moshpit

q2_types/genome_data/__init__.py

@@ -16,13 +16,14 @@
 from ._types import (
     GenomeData, Genes, Proteins, Loci, Orthologs, DNASequence, NOG
 )
-from ._methods import collate_orthologs, partition_orthologs
+from ._methods import collate_orthologs, partition_orthologs, \
+    collate_ortholog_annotations
 
 __all__ = [
     'GenomeData', 'Genes', 'Proteins', 'Loci', 'GFF3Format',
     'GenesDirectoryFormat', 'ProteinsDirectoryFormat', 'LociDirectoryFormat',
     'IntervalMetadataIterator', 'OrthologFileFmt', 'Orthologs',
     'SeedOrthologDirFmt', 'GenomeSequencesDirectoryFormat', 'DNASequence',
     'OrthologAnnotationDirFmt', 'NOG',
-    'collate_orthologs', 'partition_orthologs',
+    'collate_orthologs', 'partition_orthologs', "collate_ortholog_annotations"
     ]

q2_types/genome_data/_methods.py

@@ -12,7 +12,7 @@
 import numpy as np
 from qiime2.util import duplicate
 
-from q2_types.genome_data import SeedOrthologDirFmt
+from q2_types.genome_data import SeedOrthologDirFmt, OrthologAnnotationDirFmt
 
 
 def collate_orthologs(orthologs: SeedOrthologDirFmt) -> SeedOrthologDirFmt:
@@ -72,3 +72,17 @@ def partition_orthologs(
             partitioned_orthologs[i] = result
 
     return partitioned_orthologs
+
+
+def collate_ortholog_annotations(
+    ortholog_annotations: OrthologAnnotationDirFmt
+) -> OrthologAnnotationDirFmt:
+    # Init output
+    collated_annotations = OrthologAnnotationDirFmt()
+
+    # Copy annotations into output
+    for anno in ortholog_annotations:
+        for fp in anno.path.iterdir():
+            duplicate(fp, collated_annotations.path / fp.name)
+
+    return collated_annotations

q2_types/genome_data/tests/test_methods.py

@@ -5,12 +5,13 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+import filecmp
 import os
 
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_types.genome_data import SeedOrthologDirFmt, collate_orthologs, \
-    partition_orthologs
+    partition_orthologs, OrthologAnnotationDirFmt, collate_ortholog_annotations
 
 
 class TestOrthologsPartitionCollating(TestPluginBase):
@@ -52,3 +53,21 @@ def test_partition_orthologs_warning_message(self):
             UserWarning, "You have requested a number of.*5.*2.*2"
         ):
             partition_orthologs(orthologs, 5)
+
+    def test_collate_ortholog_annotations(self):
+        p = self.get_data_path("ortholog-annotations-collating")
+        annotations = [
+          OrthologAnnotationDirFmt(f"{p}/{letter}", mode="r")
+          for letter in ["a", "b", "c"]
+        ]
+        collated_annotations = collate_ortholog_annotations(annotations)
+
+        # assert that all files are there
+        compare = filecmp.dircmp(
+            collated_annotations.path,
+            self.get_data_path("ortholog-annotations-collating/collated")
+        )
+        self.assertListEqual(
+            compare.common,
+            [f"{letter}.annotations" for letter in ["a", "b", "c"]]
+        )