dayhoff-tools 1.1.9__tar.gz → 1.1.11__tar.gz

{dayhoff_tools-1.1.9 → dayhoff_tools-1.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.9
+Version: 1.1.11
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.1.9 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/processors.py

@@ -408,7 +408,15 @@ class MMSeqsProfileProcessor(Processor):
 
             # 9. Create subdatabase of hits from original target_db
             self._run_mmseqs_command(
-                ["mmseqs", "createsubdb", str(result_db), str(target_db), str(hits_db)],
+                [
+                    "mmseqs",
+                    "createsubdb",
+                    str(result_db),
+                    str(target_db),
+                    str(hits_db),
+                    "--subdb-mode",
+                    "1",  # Use mode 1 to extract target sequences (2nd column) from result_db
+                ],
                 "Create hits subDB from target_db",
                 run_base_dir,
             )
@@ -459,8 +467,22 @@ class MMSeqsProfileProcessor(Processor):
                 logger.info(
                     f"Cleaned up MMseqs2 temporary directory: {mmseqs_temp_dir}"
                 )
-            # The local_target_file (copy of input) inside run_base_dir will be cleaned up
-            # by the Operator when run_base_dir itself is deleted after upload.
+
+            # Clean up the copied input file (local_target_file) from the run_base_dir
+            # so it does not get uploaded with the results.
+            if local_target_file.exists():
+                try:
+                    local_target_file.unlink()
+                    logger.info(
+                        f"Cleaned up copied input file from run directory: {local_target_file}"
+                    )
+                except OSError as e:
+                    logger.error(
+                        f"Error deleting copied input file {local_target_file}: {e}"
+                    )
+
+            # The run_base_dir (containing only the final, meaningfully named output files)
+            # will be cleaned up by the Operator after its contents are uploaded.
 
         return str(
             run_base_dir

{dayhoff_tools-1.1.9 → dayhoff_tools-1.1.11}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.1.9"
+version = "1.1.11"
 description = "Common tools for all the repos at Dayhoff Labs"
 authors = [
     {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}