| |
| """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() |
|
|
|
|
