| """`casmd-report` CLI: generate DOCX + PPTX from analyze.py outputs.""" |
| from __future__ import annotations |
| import argparse |
| from pathlib import Path |
|
|
| from casmd.report.data import ReportData, PredictionSummary, load_analysis_json |
| from casmd.report.docx_writer import generate_docx |
| from casmd.report.pptx_writer import generate_pptx |
|
|
|
|
| def main(argv: list[str] | None = None) -> int: |
| p = argparse.ArgumentParser( |
| prog="casmd-report", |
| description="Generate DOCX + PPTX report from analyze.py outputs.", |
| ) |
| p.add_argument("results_json", type=Path, help="Path to results.json from analyze.py") |
| p.add_argument("--figures-dir", type=Path, required=True, |
| help="Directory containing rmsd.png / rmsf.png / rg.png") |
| p.add_argument("--name", default="casmd_run", help="Job name to display") |
| p.add_argument("--production-ns", type=float, default=100.0, |
| help="Production length in ns (for the header)") |
| p.add_argument("--interpretation", |
| default="Equilibrated protein metrics summarized below.", |
| help="One-paragraph interpretation") |
| |
| p.add_argument("--pred-backend", help="Prediction backend label (e.g. 'protenix')") |
| p.add_argument("--pred-model", type=int, default=0) |
| p.add_argument("--pred-iptm", type=float) |
| p.add_argument("--pred-ptm", type=float) |
| p.add_argument("--pred-plddt", type=float) |
| |
| p.add_argument("--docx", type=Path, help="Output DOCX path (omit to skip)") |
| p.add_argument("--pptx", type=Path, help="Output PPTX path (omit to skip)") |
| args = p.parse_args(argv) |
|
|
| if args.docx is None and args.pptx is None: |
| print("Nothing to do — pass --docx and/or --pptx.") |
| return 2 |
|
|
| analysis = load_analysis_json(args.results_json) |
| prediction = None |
| if args.pred_backend: |
| prediction = PredictionSummary( |
| backend=args.pred_backend, |
| model_id=args.pred_model, |
| iptm=args.pred_iptm, |
| ptm=args.pred_ptm, |
| plddt_mean=args.pred_plddt, |
| ) |
|
|
| figures: dict[str, Path] = {} |
| for key in ("rmsd", "rmsf", "rg"): |
| fig = args.figures_dir / f"{key}.png" |
| if fig.exists(): |
| figures[key] = fig |
|
|
| data = ReportData( |
| job_name=args.name, |
| production_ns=args.production_ns, |
| prediction=prediction, |
| analysis=analysis, |
| figures=figures, |
| interpretation=args.interpretation, |
| ) |
|
|
| if args.docx is not None: |
| generate_docx(data, args.docx) |
| print(f"DOCX: {args.docx}") |
| if args.pptx is not None: |
| generate_pptx(data, args.pptx) |
| print(f"PPTX: {args.pptx}") |
| return 0 |
|
|
|
|
| if __name__ == "__main__": |
| raise SystemExit(main()) |
|
|
