2 Commits

Author	SHA1	Message	Date
gbanyan	ee27f3ad2f	feat(02-02): add DuckDB loader and CLI evidence command for gnomAD ... - load_to_duckdb: Saves constraint DataFrame to gnomad_constraint table with provenance tracking - query_constrained_genes: Queries constrained genes by LOEUF threshold (validates GCON-03 interpretation) - evidence_cmd.py: CLI command group with gnomad subcommand (fetch->transform->load orchestration) - Checkpoint-restart: Skips processing if gnomad_constraint table exists (--force to override) - Full CLI: usher-pipeline evidence gnomad [--force] [--url URL] [--min-depth N] [--min-cds-pct N]	2026-02-11 18:19:07 +08:00
gbanyan	f33b048635	feat(01-04): add CLI entry point with setup and info commands ... - Create click-based CLI with command group (--config, --verbose options) - Add 'info' command displaying pipeline version, config hash, data source versions - Add 'setup' command orchestrating full infrastructure flow: - Load config -> create store/provenance - Fetch gene universe (with checkpoint-restart) - Map Ensembl IDs to HGNC + UniProt - Validate mapping quality gates - Save to DuckDB with provenance sidecar - Update pyproject.toml entry point to usher_pipeline.cli.main:cli - Add .gitignore for data/, *.duckdb, build artifacts, provenance files	2026-02-11 16:39:50 +08:00