dayhoff-tools 1.1.9__py3-none-any.whl → 1.1.11__py3-none-any.whl

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.dist-info → dayhoff_tools-1.1.11.dist-info}/METADATA

@@ -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.dist-info → dayhoff_tools-1.1.11.dist-info}/RECORD

@@ -11,7 +11,7 @@ dayhoff_tools/deployment/deploy_aws.py,sha256=O0gQxHioSU_sNU8T8MD4wSOPvWc--V8eRR
 dayhoff_tools/deployment/deploy_gcp.py,sha256=DxBM4sUzwPK9RWLP9bSfr38n1HHl-TVrp4TsbdN8pUA,5795
 dayhoff_tools/deployment/deploy_utils.py,sha256=StFwbqnr2_FWiKVg3xnJF4kagTHzndqqDkpaIOaAn_4,26027
 dayhoff_tools/deployment/job_runner.py,sha256=4tmdplpvqSE9bVxRWHo2U5kwkYrYod0Uwzpg2Q7qG5o,4850
-dayhoff_tools/deployment/processors.py,sha256=45CtYavKygUgNcX_zmifCWxrj1hDqp6wcy38H_ITXbg,18879
+dayhoff_tools/deployment/processors.py,sha256=qlQUElJIQSf8-m-rgZ10OIw_PQgkaNv_7XUPF1MpI5Y,19721
 dayhoff_tools/deployment/swarm.py,sha256=MGcS2_x4RNFtnVjWlU_SwNfhICz8NlGYr9cYBK4ZKDA,21688
 dayhoff_tools/embedders.py,sha256=CRgcb2z7KeeFrRQawyUZuJ4Yi0-J5jSr0hwuRhjG_FI,36513
 dayhoff_tools/fasta.py,sha256=e7xw3pInoupqCGE0-fJTOzmW_earL1M7qPyoqIPfUT4,46269
@@ -26,7 +26,7 @@ dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJq
 dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
 dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
 dayhoff_tools/warehouse.py,sha256=TqV8nex1AluNaL4JuXH5zuu9P7qmE89lSo6f_oViy6U,14965
-dayhoff_tools-1.1.9.dist-info/METADATA,sha256=gD3p_Z7SBf6ku15UJAmm6oSsEYXhBIkPAPJIETMMtzE,2224
-dayhoff_tools-1.1.9.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.1.9.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.1.9.dist-info/RECORD,,
+dayhoff_tools-1.1.11.dist-info/METADATA,sha256=gvycLzu1kBgvCDM3rF0gPB9v7_18oTHp6W6ZBPdaY9Y,2225
+dayhoff_tools-1.1.11.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.1.11.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.1.11.dist-info/RECORD,,