dayhoff-tools 1.1.12__tar.gz → 1.1.13__tar.gz

{dayhoff_tools-1.1.12 → dayhoff_tools-1.1.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.12
+Version: 1.1.13
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.1.12 → dayhoff_tools-1.1.13}/dayhoff_tools/deployment/processors.py

@@ -406,32 +406,21 @@ class MMSeqsProfileProcessor(Processor):
                 run_base_dir,
             )
 
-            # 9. Create subdatabase of hits from original target_db
+            # 9. Extract hit sequences directly to FASTA using result2flat
             self._run_mmseqs_command(
                 [
                     "mmseqs",
-                    "createsubdb",
-                    str(
-                        target_db
-                    ),  # inputDB: database to filter (all target sequences)
-                    str(result_db),  # filterDB: IDs appearing in result_db (2nd column)
-                    str(hits_db),
-                    "--subdb-mode",
-                    "1",  # Use mode 1 to extract target sequences (2nd column)
-                ],
-                "Create hits subDB from target_db",
-                run_base_dir,
-            )
-
-            # 10. Convert hit sequences to FASTA -> to intermediate file
-            self._run_mmseqs_command(
-                [
-                    "mmseqs",
-                    "convert2fasta",
-                    str(hits_db),
-                    str(intermediate_hits_fasta_file),
+                    "result2flat",
+                    str(profile_db),  # queryDB used in search
+                    str(target_db),  # targetDB
+                    str(result_db),  # resultDB
+                    str(intermediate_hits_fasta_file),  # output FASTA
+                    "--use-fasta-header",
+                    "1",
+                    "--threads",
+                    self.num_threads,
                 ],
-                "Convert hits to FASTA",
+                "Extract hit sequences to FASTA via result2flat",
                 run_base_dir,
             )
 

{dayhoff_tools-1.1.12 → dayhoff_tools-1.1.13}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.1.12"
+version = "1.1.13"
 description = "Common tools for all the repos at Dayhoff Labs"
 authors = [
     {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}