dayhoff-tools 1.1.10__tar.gz → 1.1.11__tar.gz

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Files changed (31) hide show
  1. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/processors.py +9 -1
  3. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/README.md +0 -0
  5. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/cli/utility_commands.py +0 -0
  13. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/base.py +0 -0
  14. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  15. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  16. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/job_runner.py +0 -0
  18. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/swarm.py +0 -0
  19. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/embedders.py +0 -0
  20. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/fasta.py +0 -0
  21. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/h5.py +0 -0
  23. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/intake/gcp.py +0 -0
  24. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/intake/gtdb.py +0 -0
  25. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/intake/kegg.py +0 -0
  26. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/intake/mmseqs.py +0 -0
  27. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/intake/structure.py +0 -0
  28. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/intake/uniprot.py +0 -0
  29. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/logs.py +0 -0
  30. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/sqlite.py +0 -0
  31. {dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/warehouse.py +0 -0
{dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: dayhoff-tools
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- Version: 1.1.10
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+ Version: 1.1.11
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  Summary: Common tools for all the repos at Dayhoff Labs
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  Author: Daniel Martin-Alarcon
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  Author-email: dma@dayhofflabs.com
{dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/dayhoff_tools/deployment/processors.py RENAMED
@@ -408,7 +408,15 @@ class MMSeqsProfileProcessor(Processor):
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  # 9. Create subdatabase of hits from original target_db
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  self._run_mmseqs_command(
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- ["mmseqs", "createsubdb", str(result_db), str(target_db), str(hits_db)],
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+ [
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+ "mmseqs",
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+ "createsubdb",
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+ str(result_db),
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+ str(target_db),
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+ str(hits_db),
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+ "--subdb-mode",
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+ "1", # Use mode 1 to extract target sequences (2nd column) from result_db
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+ ],
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  "Create hits subDB from target_db",
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  run_base_dir,
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  )
{dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/pyproject.toml RENAMED
@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
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  [project]
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  name = "dayhoff-tools"
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- version = "1.1.10"
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+ version = "1.1.11"
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  description = "Common tools for all the repos at Dayhoff Labs"
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  authors = [
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  {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
{dayhoff_tools-1.1.10 → dayhoff_tools-1.1.11}/README.md RENAMED
File without changes