ronboger Claude Opus 4.5 commited on
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docs: add test example using included JCVI Syn3.0 data

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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  1. GETTING_STARTED.md +16 -0
GETTING_STARTED.md CHANGED
@@ -145,6 +145,22 @@ cpr verify --check syn30 # Verify JCVI Syn3.0 result (39.6% annotation)
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  cpr verify --check all # Run all verification checks
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  ```
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  ---
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  ## FDR/FNR Threshold Reference
 
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  cpr verify --check all # Run all verification checks
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  ```
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+ ### Test with Included Data
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+
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+ The repo includes JCVI Syn3.0 sequences for testing:
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+
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+ ```bash
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+ # Test search with included FASTA (requires Zenodo data downloaded)
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+ cpr search --input data/gene_unknown/unknown_aa_seqs.fasta --output test_results.csv --fdr 0.1
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+
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+ # Or use pre-computed embeddings (faster, no model weights needed)
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+ cpr search --input data/gene_unknown/unknown_aa_seqs.npy \
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+ --database data/lookup_embeddings.npy \
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+ --output test_results.csv --fdr 0.1
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+
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+ # Expected: ~59 hits (39.6% of 149 sequences)
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+ ```
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+
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  ---
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  ## FDR/FNR Threshold Reference