83 lines
2.8 KiB
Python
83 lines
2.8 KiB
Python
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#!/usr/bin/env python3
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import argparse
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from pathlib import Path
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import sys
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def main():
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ap = argparse.ArgumentParser(description="Run identification workflow (multi-agent).")
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ap.add_argument("--hmm-id", required=True)
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ap.add_argument("--blast-id", required=True)
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ap.add_argument("--pep", required=True, help="proteins fasta")
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ap.add_argument("--pfam", required=True, help="Pfam-A.hmm")
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ap.add_argument("--out", required=True, help="workspace output dir")
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ap.add_argument("--prefix", required=True)
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ap.add_argument("--required", default="PF03110", help="comma-separated")
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ap.add_argument("--dom-i-evalue", type=float, default=1e-5)
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ap.add_argument("--hmm-cov", type=float, default=0.5)
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ap.add_argument("--cpu", type=int, default=8)
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ap.add_argument("--cut-ga", action="store_true")
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ap.add_argument("--force", action="store_true")
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args = ap.parse_args()
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# ✅ 先把项目根加入 sys.path（你的结构是 .../bba/bba/{agents,workflows,pipelines,scripts}）
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project_root = Path(__file__).resolve().parents[1]
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sys.path.insert(0, str(project_root))
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# ✅ 再 import 项目内模块（避免 “No module named agents”）
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from agents.context import RunContext
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from agents.params import IdentifyParams
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from agents.identify.merge_agent import MergeAgent
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from agents.identify.extract_agent import ExtractAgent
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from agents.identify.domain_agent import DomainAgent
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from agents.identify.report_agent import ReportAgent
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# 如果你已经加了 FinalFastaAgent（可选）
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try:
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from agents.identify.final_fasta_agent import FinalFastaAgent
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except ModuleNotFoundError:
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FinalFastaAgent = None
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from workflows.identify_workflow import IdentifyWorkflow
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ctx = RunContext(workspace=Path(args.out), prefix=args.prefix, force=args.force)
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params = IdentifyParams(
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hmm_id=args.hmm_id,
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blast_id=args.blast_id,
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pep_fasta=args.pep,
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pfam_hmm=args.pfam,
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required_pfams=args.required,
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dom_i_evalue=args.dom_i_evalue,
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hmm_cov=args.hmm_cov,
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cpu=args.cpu,
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cut_ga=args.cut_ga,
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)
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# 兼容：如果 workflow 你已经扩展成 5 个 agent（含 FinalFastaAgent）
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if FinalFastaAgent is not None:
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wf = IdentifyWorkflow(
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merge_agent=MergeAgent(),
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extract_agent=ExtractAgent(),
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domain_agent=DomainAgent(),
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final_fasta_agent=FinalFastaAgent(),
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report_agent=ReportAgent(),
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)
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else:
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wf = IdentifyWorkflow(
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merge_agent=MergeAgent(),
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extract_agent=ExtractAgent(),
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domain_agent=DomainAgent(),
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report_agent=ReportAgent(),
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)
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wf.run(ctx, params)
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print("Identify workflow finished.")
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if __name__ == "__main__":
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main()
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