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@rtlortega
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This is a continuation of the previous pull request. However, I had to start over because my previous repository was outdated compared to the latest changes.

In response to @CunliangGeng 's comments:

  • I added tests for each function (see attached screenshots).
  • I ran mypy and ruff (screenshots attached). There is one mypy error, but it originates from other files in the repository, not my changes.
  • Functions are now listed in alphabetical order.

Overview of Added Functions:

Utils (generating strain_mappings locally):

  • create_strain_mappings → Generates a JSON file for NPLinker.
  • extract_bgcs_genome_id → Extracts BGCs based on strain_id (reverse of get_bgcs_genome_mapping).
  • extract_features_metabolome_id → Extracts features based on strain_id.
  • extract_strain_metadata → Retrieves metadata from researcher-provided files.
  • merge_bgcs_features → Creates a dictionary mapping features to BGCs.

Antismash Loader:

  • get_genome_bgcs_mapping → Reverse function of the existing get_bgcs_mapping.

Final Note:
I strongly suggest keeping updated test data in the latest format within the test folder. This ensures new functions are easier to build and verify against correct data structures and types.

Screenshot 2025-01-31 at 11 37 14
Screenshot 2025-01-31 at 15 36 48
Screenshot 2025-01-31 at 15 39 33

@gcroci2
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gcroci2 commented Mar 17, 2025

I superficially reviewed this PR, and I left only one comment that needs to be addressed. I'd suggest to go through it again a bit more carefully. @CunliangGeng

@gcroci2 gcroci2 merged commit 1fe11ed into NPLinker:dev Mar 17, 2025
@github-project-automation github-project-automation bot moved this to Done in dev Mar 17, 2025
liannette added a commit to liannette/nplinker that referenced this pull request Mar 18, 2025
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