#!/usr/bin/env python3
"""
RNA-seq Alignment Skill Runner

Executes the RNA-seq alignment stage as a skill.
"""

import argparse
import json
import subprocess
import sys
from pathlib import Path
from typing import Dict, Any


def load_config(config_path: Path) -> Dict[str, Any]:
    """Load skill configuration"""
    import yaml
    with open(config_path, 'r') as f:
        return yaml.safe_load(f)


def run_skill(
    input_dir: Path,
    hisat2_index: Path,
    output_dir: Path,
    prefix: str = "",
    cpu: int = 4,
    sample_config: Path = None,
    job_id: str = "unknown"
) -> Dict[str, Any]:
    """Run the RNA-seq alignment skill"""
    
    # Import the main module
    sys.path.insert(0, str(Path(__file__).parent.parent.parent / "apps" / "cli"))
    from run_rnaseq_align import main as align_main
    
    # Build arguments
    args = [
        "-i", str(input_dir),
        "-x", str(hisat2_index),
        "-o", str(output_dir),
        "-j", job_id,
        "-p", prefix,
        "-t", str(cpu)
    ]
    
    if sample_config:
        args.extend(["--sample-config", str(sample_config)])
    
    # Run the alignment
    sys.argv = ["run_rnaseq_align.py"] + args
    align_main()
    
    # Load and return manifest
    manifest_path = output_dir.parent / "final" / f"{prefix}.rnaseq_align.manifest.json"
    if manifest_path.exists():
        with open(manifest_path, 'r') as f:
            return json.load(f)
    
    return {"status": "failed", "error": "Manifest not found"}


def main():
    parser = argparse.ArgumentParser(description="RNA-seq Alignment Skill")
    parser.add_argument("-i", "--input", required=True, help="Input directory with clean FASTQ")
    parser.add_argument("-x", "--hisat2-index", required=True, help="HISAT2 index prefix")
    parser.add_argument("-o", "--output", required=True, help="Output directory")
    parser.add_argument("-j", "--job-id", default="unknown", help="Job ID")
    parser.add_argument("-p", "--prefix", default="", help="Output prefix")
    parser.add_argument("-t", "--cpu", type=int, default=4, help="CPU threads")
    parser.add_argument("-c", "--config", help="Sample config YAML")
    
    args = parser.parse_args()
    
    result = run_skill(
        input_dir=Path(args.input),
        hisat2_index=Path(args.hisat2_index),
        output_dir=Path(args.output),
        prefix=args.prefix,
        cpu=args.cpu,
        sample_config=Path(args.config) if args.config else None,
        job_id=args.job_id
    )
    
    print(json.dumps(result, indent=2))
    return 0 if result.get("status") == "success" else 1


if __name__ == "__main__":
    sys.exit(main())