67 lines
2.3 KiB
Python
Executable File
67 lines
2.3 KiB
Python
Executable File
#!/usr/bin/env python3
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"""Generate or open a formal RNA-seq evidence report."""
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from __future__ import annotations
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import argparse
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import sys
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from pathlib import Path
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PROJECT_ROOT = Path(__file__).absolute().parents[2]
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if str(PROJECT_ROOT) not in sys.path:
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sys.path.insert(0, str(PROJECT_ROOT))
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from gfa_core.rnaseq_report import NoSuccessfulRNASeqEvidence, generate_rnaseq_report
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def _csv(value: str) -> list[str] | None:
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values = [item.strip() for item in str(value or "").split(",") if item.strip()]
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return values or None
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def main() -> int:
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parser = argparse.ArgumentParser(
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description="Generate a deterministic formal RNA-seq result report from successful manifests."
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)
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parser.add_argument("--workspace", required=True, help="RNA-seq job workspace containing final/")
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parser.add_argument("--prefix", required=True, help="RNA-seq output prefix")
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parser.add_argument("--job-id", default="")
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parser.add_argument("--rnaseq-scope-id", default="")
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parser.add_argument(
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"--expected-stages",
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default="",
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help="Comma-separated stages selected for the current RNA-seq batch",
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)
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parser.add_argument("--action", choices=("generate", "open"), default="generate")
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parser.add_argument("--no-model", action="store_true", help="Disable optional LLM language enhancement")
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parser.add_argument("--log-file", default="", help="Accepted for pipeline runner compatibility")
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args = parser.parse_args()
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try:
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result = generate_rnaseq_report(
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Path(args.workspace),
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args.prefix,
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rnaseq_scope_id=args.rnaseq_scope_id,
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expected_stages=_csv(args.expected_stages),
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use_model=not args.no_model,
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action=args.action,
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job_id=args.job_id,
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)
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except NoSuccessfulRNASeqEvidence as exc:
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print(str(exc), file=sys.stderr)
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return 2
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except Exception as exc:
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print(f"RNA-seq 结果报告生成失败：{type(exc).__name__}: {exc}", file=sys.stderr)
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return 1
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reuse = "（复用最新报告）" if result.reused else ""
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print(
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f"RNA-seq 结果报告已就绪{reuse}: {result.report_path} "
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f"[coverage={result.coverage_status}, stages={','.join(result.included_stages)}]"
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)
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return 0
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if __name__ == "__main__":
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raise SystemExit(main())
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