dayhoff-tools 1.1.11__py3-none-any.whl → 1.1.13__py3-none-any.whl

dayhoff_tools/deployment/processors.py

@@ -406,30 +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(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,
-            )
-
-            # 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-1.1.11.dist-info → dayhoff_tools-1.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.11
+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-1.1.11.dist-info → dayhoff_tools-1.1.13.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=qlQUElJIQSf8-m-rgZ10OIw_PQgkaNv_7XUPF1MpI5Y,19721
+dayhoff_tools/deployment/processors.py,sha256=KNtAIshHDHEEipPdoGoFjVt4BjfeNZhADShstJ-1Pa4,19483
 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-1.1.11.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,,
+dayhoff_tools-1.1.13.dist-info/METADATA,sha256=wk4uAkCGnocM0U6HOmlUeVSEqyPV4keb0dvgSVEiIZo,2225
+dayhoff_tools-1.1.13.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.1.13.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.1.13.dist-info/RECORD,,