45 lines
1.5 KiB
Python
45 lines
1.5 KiB
Python
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# scripts/run_blast_pipeline.py
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import argparse
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from pathlib import Path
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import sys
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sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
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from pipelines.blast_pipeline import run_blastp_pipeline
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def main():
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ap = argparse.ArgumentParser("--interactive", action="store_true", help="交互式设置阈值（回车=默认值）")
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ap.add_argument("--ref", required=True, help="参考家族蛋白 fasta（如 SPL_Ath.fasta）")
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ap.add_argument("--query", required=True, help="目标物种全蛋白 fasta（如 Ft.pep.fasta）")
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ap.add_argument("--out", required=True, help="输出目录")
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ap.add_argument("--prefix", required=True, help="输出前缀（如 Ft.SPL）")
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ap.add_argument("--evalue", type=float, default=1e-5)
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ap.add_argument("--pident", type=float, default=30.0)
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ap.add_argument("--qcov", type=float, default=40.0)
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ap.add_argument("--scov", type=float, default=40.0)
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ap.add_argument("--threads", type=int, default=8)
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args = ap.parse_args()
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out = run_blastp_pipeline(
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reference_fasta=args.ref,
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query_fasta=args.query,
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out_dir=args.out,
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prefix=args.prefix,
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evalue_max=args.evalue,
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pident_min=args.pident,
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qcov_min=args.qcov,
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scov_min=args.scov,
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threads=args.threads,
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)
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print("=== DONE ===")
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print("blastout:", out.blastout)
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print("filtered_tsv:", out.filtered_tsv)
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print("id_list:", out.id_list)
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print(f"hits: {out.hit_count}, unique_ids: {out.unique_id_count}")
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if __name__ == "__main__":
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main()
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