# Genomic Consultant

Early design for a personal genomic risk and drug–interaction decision support system. Specs are sourced from `genomic_decision_support_system_spec_v0.1.md`.

## Vision (per spec)
- Phase 1: trio variant calling, annotation, queryable genomic DB, initial ACMG evidence tagging.
- Phase 2: pharmacogenomics genotype-to-phenotype mapping plus drug–drug interaction checks.
- Phase 3: supplement/herb normalization and interaction risk layering.
- Phase 4: LLM-driven query orchestration and report generation.

## Repository Layout
- `docs/` — system architecture notes, phase plans, data models (work in progress).
- `configs/` — example ACMG config and gene panel JSON.
- `configs/phenotype_to_genes.example.json` — placeholder phenotype/HPO → gene mappings.
- `configs/phenotype_to_genes.hpo_seed.json` — seed HPO mappings (replace with full HPO/GenCC derived panels).
- `sample_data/` — tiny annotated TSV for demo.
- `src/genomic_consultant/` — Python scaffolding (pipelines, store, panel lookup, ACMG tagging, reporting).
- `genomic_decision_support_system_spec_v0.1.md` — original requirements draft.

## Contributing/next steps
1. Finalize Phase 1 tech selection (variant caller, annotation stack, reference/DB versions).
2. Stand up the Phase 1 pipelines and minimal query API surface.
3. Add ACMG evidence tagging config and human-review logging.
4. Layer in PGx/DDI and supplement modules per later phases.

Data safety: keep genomic/clinical data local; the `.gitignore` blocks common genomic outputs by default.

## Quickstart (CLI scaffolding)
```
pip install -e .

# 1) Show trio calling plan (commands only; not executed)
genomic-consultant plan-call \
  --sample proband:/data/proband.bam \
  --sample father:/data/father.bam \
  --sample mother:/data/mother.bam \
  --reference /refs/GRCh38.fa \
  --workdir /tmp/trio

# 1b) Execute calling plan (requires GATK installed) and emit run log
genomic-consultant run-call \
  --sample proband:/data/proband.bam \
  --sample father:/data/father.bam \
  --sample mother:/data/mother.bam \
  --reference /refs/GRCh38.fa \
  --workdir /tmp/trio \
  --log /tmp/trio/run_call_log.json \
  --probe-tools

# 2) Show annotation plan for a joint VCF
genomic-consultant plan-annotate \
  --vcf /tmp/trio/trio.joint.vcf.gz \
  --workdir /tmp/trio/annot \
  --prefix trio \
  --reference /refs/GRCh38.fa

# 2b) Execute annotation plan (requires VEP, bcftools) with run log
genomic-consultant run-annotate \
  --vcf /tmp/trio/trio.joint.vcf.gz \
  --workdir /tmp/trio/annot \
  --prefix trio \
  --reference /refs/GRCh38.fa \
  --log /tmp/trio/annot/run_annot_log.json \
  --probe-tools

# 3) Demo panel report using sample data (panel file)
genomic-consultant panel-report \
  --tsv sample_data/example_annotated.tsv \
  --panel configs/panel.example.json \
  --acmg-config configs/acmg_config.example.yaml \
  --individual-id demo \
  --format markdown \
  --log /tmp/panel_log.json

# 3b) Demo panel report using phenotype mapping (HPO)
genomic-consultant panel-report \
  --tsv sample_data/example_annotated.tsv \
  --phenotype-id HP:0000365 \
  --phenotype-mapping configs/phenotype_to_genes.hpo_seed.json \
  --acmg-config configs/acmg_config.example.yaml \
  --individual-id demo \
  --format markdown

# 3c) Merge multiple phenotype→gene mappings into one
genomic-consultant build-phenotype-mapping \
  --output configs/phenotype_to_genes.merged.json \
  configs/phenotype_to_genes.example.json configs/phenotype_to_genes.hpo_seed.json

# 4) End-to-end Phase 1 pipeline (optionally skip call/annotate; use sample TSV)
genomic-consultant phase1-run \
  --tsv sample_data/example_annotated.tsv \
  --skip-call --skip-annotate \
  --panel configs/panel.example.json \
  --acmg-config configs/acmg_config.example.yaml \
  --workdir runtime \
  --prefix demo

# Run tests
pytest
```

### Optional Parquet-backed store
Install pandas to enable Parquet ingestion:
```
pip install -e .[store]
```

### Notes on VEP plugins (SpliceAI/CADD)
- The annotation plan already queries `SpliceAI` and `CADD_PHRED` fields; ensure your VEP run includes plugins/flags that produce them, e.g.:
  - `--plugin SpliceAI,snv=/path/to/spliceai.snv.vcf.gz,indel=/path/to/spliceai.indel.vcf.gz`
  - `--plugin CADD,/path/to/whole_genome_SNVs.tsv.gz,/path/to/InDels.tsv.gz`
- Pass these via `--plugin` and/or `--extra-flag` on `run-annotate` / `plan-annotate` to embed fields into the TSV.