dayhoff-tools 1.1.18__py3-none-any.whl → 1.1.19__py3-none-any.whl

dayhoff_tools/deployment/processors.py

@@ -405,16 +405,20 @@ class MMSeqsProfileProcessor(Processor):
                 run_base_dir,
             )
 
-            # 9. Extract hit sequences directly to FASTA using result2flat
+            # 9. Extract hit sequences directly to FASTA using createseqfiledb
             self._run_mmseqs_command(
                 [
                     "mmseqs",
                     "createseqfiledb",
-                    str(result_db),  # resultDB containing target hits
-                    str(target_db),  # targetDB containing actual sequences
-                    str(intermediate_hits_fasta_file),  # output FASTA
-                    "--db-output",
-                    "1",  # Output in FASTA format
+                    str(target_db),  # <i:sequenceDB> - The DB to pull sequences from
+                    str(
+                        result_db
+                    ),  # <i:resultDB> - Contains IDs of target sequences to pull
+                    str(
+                        intermediate_hits_fasta_file
+                    ),  # <o:fastaDB> - Output FASTA file
+                    "--threads",  # createseqfiledb supports --threads
+                    self.num_threads,
                 ],
                 "Extract hit sequences to FASTA via createseqfiledb",
                 run_base_dir,

{dayhoff_tools-1.1.18.dist-info → dayhoff_tools-1.1.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.1.18
+Version: 1.1.19
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.1.18.dist-info → dayhoff_tools-1.1.19.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=1msmRHjSToup2f7DQVpAfpFkBMSzMh1YG_7WJEpChWg,19382
+dayhoff_tools/deployment/processors.py,sha256=4a8fYFilcbBGAVUeowjL5n-Pa7NIL3Jmhs69lCQIkpQ,19554
 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-1.1.18.dist-info/METADATA,sha256=9uJXFcLDGpuxssU_xBvmehDR58gPs-gFtKShHhEw4u4,2225
-dayhoff_tools-1.1.18.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.1.18.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.1.18.dist-info/RECORD,,
+dayhoff_tools-1.1.19.dist-info/METADATA,sha256=40SO5LPPs3GIs_bHfr5jt-TpZUb05-5EHz6Uo09TdxI,2225
+dayhoff_tools-1.1.19.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.1.19.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.1.19.dist-info/RECORD,,