54 lines
1.6 KiB
Python
Executable File
54 lines
1.6 KiB
Python
Executable File
#!/usr/bin/env python3
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"""Skill wrapper for the rnaseq_fgsea CLI stage."""
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from __future__ import annotations
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import argparse
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import subprocess
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import sys
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from pathlib import Path
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PROJECT_ROOT = Path(__file__).resolve().parents[2]
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CLI = PROJECT_ROOT / "apps" / "cli" / "run_rnaseq_fgsea.py"
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def main() -> int:
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parser = argparse.ArgumentParser(description="RNA-seq fgsea skill wrapper")
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parser.add_argument("--workspace", required=True, help="workspace/<job_id> directory")
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parser.add_argument("--prefix", default="")
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parser.add_argument("--job-id", default="")
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parser.add_argument("--comparison", default="")
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parser.add_argument("--gene2ko", default="")
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parser.add_argument("--kegg-cache-dir", default="")
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parser.add_argument("--min-size", type=int, default=15)
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parser.add_argument("--max-size", type=int, default=500)
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parser.add_argument("--nperm", type=int, default=10000)
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parser.add_argument("--seed", type=int, default=1)
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args = parser.parse_args()
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cmd = [
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sys.executable,
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str(CLI),
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"--workspace",
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args.workspace,
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"--min-size",
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str(args.min_size),
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"--max-size",
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str(args.max_size),
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"--nperm",
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str(args.nperm),
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"--seed",
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str(args.seed),
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]
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for key in ("prefix", "job_id", "comparison", "gene2ko", "kegg_cache_dir"):
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value = getattr(args, key)
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if value:
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cmd.extend(["--" + key.replace("_", "-"), value])
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return subprocess.call(cmd, cwd=str(PROJECT_ROOT))
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if __name__ == "__main__":
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raise SystemExit(main())
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