#!/usr/bin/env python3 """Create a GEO-style task case from counts + sample metadata. Example: PYTHONPATH=src:envs uv run python envs/pathway_analysis_env/scripts/create_geo_task.py \ --task-id gseXXXX_example \ --accession GSEXXXX \ --summary "Short study summary" \ --counts-file /path/to/counts.csv.gz \ --metadata-csv /path/to/samples.csv \ --reference-condition control \ --alternate-condition treated """ from __future__ import annotations import argparse import csv import json import shutil from pathlib import Path from typing import Dict, List, Tuple DEFAULT_LIBRARIES = ["MSigDB_Hallmark_2020", "KEGG_2021_Human", "Reactome_2022"] def _read_metadata_csv(path: Path) -> Tuple[List[str], Dict[str, str], List[str]]: with path.open("r", encoding="utf-8", newline="") as f: reader = csv.DictReader(f) fields = set(reader.fieldnames or []) required = {"sample_id", "condition"} missing = required - fields if missing: raise ValueError( f"{path} is missing required columns: {sorted(missing)} " "(required: sample_id, condition)" ) sample_ids: List[str] = [] sample_metadata: Dict[str, str] = {} conditions: List[str] = [] seen_conditions = set() for row in reader: sample_id = (row.get("sample_id") or "").strip() condition = (row.get("condition") or "").strip() if not sample_id or not condition: raise ValueError( f"{path} has empty sample_id/condition row: {row!r}" ) sample_ids.append(sample_id) sample_metadata[sample_id] = condition if condition not in seen_conditions: seen_conditions.add(condition) conditions.append(condition) if not sample_ids: raise ValueError(f"{path} has no sample rows") return sample_ids, sample_metadata, conditions def _counts_dest_name(src: Path) -> str: name = src.name if name.endswith(".csv") or name.endswith(".csv.gz"): return name return f"{src.stem}.csv.gz" if src.suffix == ".gz" else f"{src.name}.csv.gz" def main() -> None: parser = argparse.ArgumentParser( description="Create a GEO task case JSON from counts + sample metadata." ) parser.add_argument("--task-id", required=True, help="Folder id under data/geo_eval/") parser.add_argument("--accession", required=True, help="Study accession (e.g. GSE216540)") parser.add_argument("--summary", required=True, help="Short human-readable study summary") parser.add_argument("--counts-file", type=Path, required=True, help="Path to counts .csv/.csv.gz") parser.add_argument( "--metadata-csv", type=Path, required=True, help="CSV with columns: sample_id,condition", ) parser.add_argument("--reference-condition", required=True, help="Reference group name") parser.add_argument("--alternate-condition", required=True, help="Alternate group name") parser.add_argument( "--geo-ref-url", default="", help="Optional GEO URL; default is generated from accession", ) parser.add_argument( "--libraries", default=",".join(DEFAULT_LIBRARIES), help="Comma-separated Enrichr libraries", ) parser.add_argument( "--out-dir", type=Path, default=Path("envs/pathway_analysis_env/data/geo_eval"), help="Directory that stores task folders", ) parser.add_argument( "--copy-counts", action="store_true", help="Copy counts file into task folder (default behavior)", ) parser.add_argument( "--no-copy-counts", action="store_true", help="Do not copy counts file (use existing file under task folder)", ) args = parser.parse_args() if args.reference_condition == args.alternate_condition: raise ValueError("reference-condition and alternate-condition must be different") sample_ids, sample_metadata, conditions = _read_metadata_csv(args.metadata_csv) if args.reference_condition not in conditions: raise ValueError( f"reference-condition '{args.reference_condition}' not found in metadata conditions {conditions}" ) if args.alternate_condition not in conditions: raise ValueError( f"alternate-condition '{args.alternate_condition}' not found in metadata conditions {conditions}" ) task_dir = args.out_dir / args.task_id task_dir.mkdir(parents=True, exist_ok=True) counts_src = args.counts_file.resolve() if not counts_src.exists(): raise FileNotFoundError(f"counts file not found: {counts_src}") should_copy = not args.no_copy_counts if args.copy_counts: should_copy = True if should_copy: counts_name = _counts_dest_name(counts_src) counts_dst = task_dir / counts_name shutil.copy2(counts_src, counts_dst) else: counts_dst = counts_src if task_dir not in counts_dst.parents: raise ValueError( "--no-copy-counts requires counts-file to already be inside task folder" ) counts_rel = f"geo_eval/{args.task_id}/{counts_dst.name}" case_name = f"{args.accession.lower()}_case.json" case_path = task_dir / case_name ref_url = args.geo_ref_url.strip() or f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={args.accession}" libraries = [s.strip() for s in args.libraries.split(",") if s.strip()] if not libraries: libraries = DEFAULT_LIBRARIES case = { "case_id": args.task_id, "strict_mode": False, "experiment_metadata": { "accession": args.accession, "reference": ref_url, "summary": args.summary, }, "counts_file": counts_rel, "sample_ids": sample_ids, "sample_metadata": sample_metadata, "conditions": conditions, "default_contrast": { "reference": args.reference_condition, "alternate": args.alternate_condition, }, "analysis_options": { "min_total_count": 10, "padj_alpha": 0.05, "de_query_direction": "both", }, "enrichr_libraries": libraries, "true_pathway": "Unknown (GEO benchmark)", } case_path.write_text(json.dumps(case, indent=2) + "\n", encoding="utf-8") print(f"[ok] wrote case: {case_path}") print(f"[ok] counts file: {counts_dst}") print( "[next] append to manifest:\n" " PYTHONPATH=src:envs uv run python " "envs/pathway_analysis_env/scripts/append_task_to_manifest.py " f"--manifest envs/pathway_analysis_env/data/eval_manifest_geo3.json " f"--episode-id {args.task_id} --case-file {counts_rel.rsplit('/', 1)[0]}/{case_name} " '--hypothesis "your expected theme"' ) if __name__ == "__main__": main()