dayhoff-tools 1.1.18__tar.gz → 1.1.19__tar.gz

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Files changed (31) hide show
  1. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/processors.py +10 -6
  3. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/README.md +0 -0
  5. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/cli/utility_commands.py +0 -0
  13. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/base.py +0 -0
  14. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  15. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  16. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/job_runner.py +0 -0
  18. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/swarm.py +0 -0
  19. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/embedders.py +0 -0
  20. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/fasta.py +0 -0
  21. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/h5.py +0 -0
  23. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/intake/gcp.py +0 -0
  24. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/intake/gtdb.py +0 -0
  25. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/intake/kegg.py +0 -0
  26. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/intake/mmseqs.py +0 -0
  27. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/intake/structure.py +0 -0
  28. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/intake/uniprot.py +0 -0
  29. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/logs.py +0 -0
  30. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/sqlite.py +0 -0
  31. {dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/warehouse.py +0 -0
{dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/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: 1.1.18
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+ Version: 1.1.19
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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-1.1.18 → dayhoff_tools-1.1.19}/dayhoff_tools/deployment/processors.py RENAMED
@@ -405,16 +405,20 @@ class MMSeqsProfileProcessor(Processor):
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  run_base_dir,
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  )
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- # 9. Extract hit sequences directly to FASTA using result2flat
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+ # 9. Extract hit sequences directly to FASTA using createseqfiledb
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  self._run_mmseqs_command(
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  [
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  "mmseqs",
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  "createseqfiledb",
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- str(result_db), # resultDB containing target hits
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- str(target_db), # targetDB containing actual sequences
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- str(intermediate_hits_fasta_file), # output FASTA
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- "--db-output",
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- "1", # Output in FASTA format
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+ str(target_db), # <i:sequenceDB> - The DB to pull sequences from
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+ str(
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+ result_db
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+ ), # <i:resultDB> - Contains IDs of target sequences to pull
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+ str(
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+ intermediate_hits_fasta_file
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+ ), # <o:fastaDB> - Output FASTA file
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+ "--threads", # createseqfiledb supports --threads
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+ self.num_threads,
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  ],
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  "Extract hit sequences to FASTA via createseqfiledb",
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  run_base_dir,
{dayhoff_tools-1.1.18 → dayhoff_tools-1.1.19}/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 = "1.1.18"
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+ version = "1.1.19"
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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-1.1.18 → dayhoff_tools-1.1.19}/README.md RENAMED
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