feat: scaffold for all annotations with reasonable structure#13
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shloknatarajan merged 47 commits intoDaneshjouLab:mainfrom Jul 1, 2025
Merged
feat: scaffold for all annotations with reasonable structure#13shloknatarajan merged 47 commits intoDaneshjouLab:mainfrom
shloknatarajan merged 47 commits intoDaneshjouLab:mainfrom
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…ations - Implement module-level caching for get_true_variants() to avoid repeated JSON file loading - Fix type annotations across multiple files to use Optional[T] instead of T = None - Add comprehensive efficiency analysis report documenting all identified issues - Add test script to verify caching functionality works correctly This addresses the critical efficiency issue where JSON files were loaded on every function call, causing unnecessary disk I/O operations. The caching implementation uses lazy loading with proper error handling for missing files. Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>
- Add DrugAnnotation and DrugAnnotationList models to src/variants.py - Create new drug_annotation_extraction.py component with detailed field extraction - Integrate drug annotation extraction into variant association pipeline - Add comprehensive test script for verification - Follow existing LLM infrastructure patterns (Generator/Parser) - Extract detailed pharmacogenomic fields matching provided schema Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>
- Modified extract_drug_annotations to loop through variants one at a time - Each variant now gets individual LLM processing for better control - Added SingleDrugAnnotation model for individual variant processing - Updated logging to show individual variant processing progress - Maintains same output quality while providing cleaner extraction per variant - Updated test script to reflect individual processing approach Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>
…ation-extraction Add drug annotation extraction component for variants with drug associations
…-improvements Efficiency improvements: Cache JSON loading and fix type annotations
…ents - Add PhenotypeAnnotation and FunctionalAnnotation data models to variants.py - Create phenotype_annotation_extraction.py with detailed extraction logic - Create functional_annotation_extraction.py with mechanistic annotation logic - Update variant_association_pipeline.py to integrate new extraction components - Follow existing drug annotation extraction patterns - Use detailed prompt templates from annotation_prompts.md - Process variants individually for better control and cleaner extraction - Include proper error handling and logging throughout Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>
- Move test_imports.py and test_new_annotations.py to tests/ directory - Clean up temporary converted notebook file - Follow proper repository structure conventions Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>
- Fix Python path resolution for tests running from tests/ subdirectory - Ensure tests can properly import src modules from new location - Verify all tests pass after organizational changes Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>
…functional-extraction feat: implement phenotype and functional annotation extraction components
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Annotation pipeline works and saves outputs