92 lines
2.6 KiB
Python
Executable File
92 lines
2.6 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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RNA-seq Alignment Skill Runner
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Executes the RNA-seq alignment stage as a skill.
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"""
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import argparse
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import json
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import subprocess
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import sys
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from pathlib import Path
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from typing import Dict, Any
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def load_config(config_path: Path) -> Dict[str, Any]:
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"""Load skill configuration"""
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import yaml
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with open(config_path, 'r') as f:
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return yaml.safe_load(f)
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def run_skill(
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input_dir: Path,
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hisat2_index: Path,
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output_dir: Path,
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prefix: str = "",
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cpu: int = 4,
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sample_config: Path = None,
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job_id: str = "unknown"
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) -> Dict[str, Any]:
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"""Run the RNA-seq alignment skill"""
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# Import the main module
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sys.path.insert(0, str(Path(__file__).parent.parent.parent / "apps" / "cli"))
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from run_rnaseq_align import main as align_main
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# Build arguments
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args = [
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"-i", str(input_dir),
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"-x", str(hisat2_index),
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"-o", str(output_dir),
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"-j", job_id,
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"-p", prefix,
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"-t", str(cpu)
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]
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if sample_config:
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args.extend(["--sample-config", str(sample_config)])
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# Run the alignment
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sys.argv = ["run_rnaseq_align.py"] + args
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align_main()
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# Load and return manifest
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manifest_path = output_dir.parent / "final" / f"{prefix}.rnaseq_align.manifest.json"
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if manifest_path.exists():
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with open(manifest_path, 'r') as f:
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return json.load(f)
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return {"status": "failed", "error": "Manifest not found"}
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def main():
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parser = argparse.ArgumentParser(description="RNA-seq Alignment Skill")
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parser.add_argument("-i", "--input", required=True, help="Input directory with clean FASTQ")
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parser.add_argument("-x", "--hisat2-index", required=True, help="HISAT2 index prefix")
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parser.add_argument("-o", "--output", required=True, help="Output directory")
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parser.add_argument("-j", "--job-id", default="unknown", help="Job ID")
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parser.add_argument("-p", "--prefix", default="", help="Output prefix")
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parser.add_argument("-t", "--cpu", type=int, default=4, help="CPU threads")
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parser.add_argument("-c", "--config", help="Sample config YAML")
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args = parser.parse_args()
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result = run_skill(
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input_dir=Path(args.input),
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hisat2_index=Path(args.hisat2_index),
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output_dir=Path(args.output),
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prefix=args.prefix,
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cpu=args.cpu,
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sample_config=Path(args.config) if args.config else None,
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job_id=args.job_id
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)
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print(json.dumps(result, indent=2))
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return 0 if result.get("status") == "success" else 1
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if __name__ == "__main__":
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sys.exit(main())
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