43 lines
1.3 KiB
Python
Executable File
43 lines
1.3 KiB
Python
Executable File
# scripts/run_hmm_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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# 把 bba/bba 这一层加入 Python 搜索路径，这样才能 import pipelines.*
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sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
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from pipelines.hmm_pipeline import run_hmmsearch_pipeline
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def main():
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ap = argparse.ArgumentParser()
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ap.add_argument("--hmm", required=True)
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ap.add_argument("--pep", required=True)
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ap.add_argument("--out", required=True)
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ap.add_argument("--prefix", required=True)
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ap.add_argument("--cpu", type=int, default=4)
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ap.add_argument("--no-cut-tc", action="store_true")
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ap.add_argument("--full-evalue", type=float, default=None)
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ap.add_argument("--dom-i-evalue", type=float, default=None)
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args = ap.parse_args()
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out = run_hmmsearch_pipeline(
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hmm_profile=args.hmm,
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protein_fasta=args.pep,
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out_dir=args.out,
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prefix=args.prefix,
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cut_tc=not args.no_cut_tc,
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cpu=args.cpu,
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full_evalue_max=args.full_evalue,
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dom_i_evalue_max=args.dom_i_evalue,
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)
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print("=== DONE ===")
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print("domtblout:", out.domtblout)
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print("hmmout:", out.hmmout)
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print("filter:", out.domtblout_filter)
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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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