Refactor: Unified pipeline execution, simplified UI, and fixed Docker config
- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency. - Backend: Changed output format to ZIP and added auto-cleanup of intermediate files. - Backend: Fixed language parameter passing in API and tasks. - Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views. - Frontend: Implemented simulated progress bar for better UX. - Frontend: Restored One-click load button and added result file structure documentation. - Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml. - Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.
This commit is contained in:
zly
1
tools/crispr_cas_analysis/scripts/__init__.py
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tools/crispr_cas_analysis/scripts/__init__.py
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"""Scripts for CRISPR-Cas detection and analysis"""
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tools/crispr_cas_analysis/scripts/detect_crispr.py
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tools/crispr_cas_analysis/scripts/detect_crispr.py
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#!/usr/bin/env python3
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"""
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CRISPR-Cas Detection Wrapper
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Wrapper for CRISPRCasFinder or similar tools to detect CRISPR arrays and Cas genes.
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"""
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import argparse
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import json
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import logging
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import shutil
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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, List, Any
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# Configure logging
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logging.basicConfig(
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level=logging.INFO,
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format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
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)
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logger = logging.getLogger(__name__)
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def parse_args():
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parser = argparse.ArgumentParser(description="Detect CRISPR arrays and Cas genes in genome")
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parser.add_argument("--input", "-i", type=Path, required=True, help="Input genome file (.fna)")
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parser.add_argument("--output", "-o", type=Path, required=True, help="Output JSON results file")
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parser.add_argument("--tool-path", type=Path, default=None, help="Path to CRISPRCasFinder.pl")
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parser.add_argument("--mock", action="store_true", help="Use mock data (for testing without external tools)")
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return parser.parse_args()
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def check_dependencies(tool_path: Path = None) -> bool:
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"""Check if CRISPRCasFinder is available"""
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if tool_path and tool_path.exists():
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return True
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# Check in PATH
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if shutil.which("CRISPRCasFinder.pl"):
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return True
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return False
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def generate_mock_results(genome_file: Path) -> Dict[str, Any]:
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"""Generate mock CRISPR results for testing"""
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logger.info(f"Generating mock CRISPR results for {genome_file.name}")
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strain_id = genome_file.stem
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return {
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"strain_id": strain_id,
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"cas_systems": [
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{
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"type": "I-E",
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"subtype": "I-E",
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"position": "contig_1:15000-25000",
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"genes": ["cas1", "cas2", "cas3", "casA", "casB", "casC", "casD", "casE"]
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}
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],
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"arrays": [
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{
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"id": "CRISPR_1",
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"contig": "contig_1",
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"start": 12345,
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"end": 12678,
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"consensus_repeat": "GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC",
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"num_spacers": 5,
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"spacers": [
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{"sequence": "ATGCGTCGACATGCGTCGACATGCGTCGAC", "position": 1},
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{"sequence": "CGTAGCTAGCCGTAGCTAGCCGTAGCTAGC", "position": 2},
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{"sequence": "TGCATGCATGTGCATGCATGTGCATGCATG", "position": 3},
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{"sequence": "GCTAGCTAGCGCTAGCTAGCGCTAGCTAGC", "position": 4},
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{"sequence": "AAAAATTTTTAAAAATTTTTAAAAATTTTT", "position": 5}
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]
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},
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{
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"id": "CRISPR_2",
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"contig": "contig_2",
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"start": 50000,
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"end": 50500,
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"consensus_repeat": "GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC",
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"num_spacers": 8,
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"spacers": [
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{"sequence": "CCCGGGAAACCCGGGAAACCCGGGAAA", "position": 1}
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]
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}
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],
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"summary": {
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"has_cas": True,
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"has_crispr": True,
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"num_arrays": 2,
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"num_spacers": 13,
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"cas_types": ["I-E"]
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},
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"metadata": {
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"tool": "CRISPRCasFinder",
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"version": "Mock-v1.0",
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"date": "2025-01-14"
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}
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}
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def run_crisprcasfinder(input_file: Path, output_file: Path, tool_path: Path = None):
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"""Run actual CRISPRCasFinder tool (Placeholder)"""
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# This would implement the actual subprocess call to CRISPRCasFinder.pl
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# For now, we raise NotImplementedError unless mock is used
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raise NotImplementedError("Real tool integration not yet implemented. Use --mock flag.")
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def main():
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args = parse_args()
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if not args.input.exists():
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logger.error(f"Input file not found: {args.input}")
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sys.exit(1)
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# Create parent directory for output if needed
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args.output.parent.mkdir(parents=True, exist_ok=True)
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try:
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if args.mock:
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results = generate_mock_results(args.input)
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else:
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if not check_dependencies(args.tool_path):
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logger.warning("CRISPRCasFinder not found. Falling back to mock data.")
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results = generate_mock_results(args.input)
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else:
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# Real implementation would go here
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run_crisprcasfinder(args.input, args.output, args.tool_path)
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return
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# Write results
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with open(args.output, 'w') as f:
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json.dump(results, f, indent=2)
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logger.info(f"Results written to {args.output}")
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except Exception as e:
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logger.error(f"Error executing CRISPR detection: {e}")
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sys.exit(1)
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if __name__ == "__main__":
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main()
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166
tools/crispr_cas_analysis/scripts/fusion_analysis.py
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tools/crispr_cas_analysis/scripts/fusion_analysis.py
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#!/usr/bin/env python3
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"""
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CRISPR-Toxin Fusion Analysis
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Analyzes associations between CRISPR spacers and toxin genes.
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"""
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import argparse
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import json
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import logging
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import sys
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from pathlib import Path
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from typing import Dict, List, Any
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# Configure logging
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logging.basicConfig(
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level=logging.INFO,
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format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
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)
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logger = logging.getLogger(__name__)
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def parse_args():
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parser = argparse.ArgumentParser(description="Analyze CRISPR-Toxin associations")
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parser.add_argument("--crispr-results", type=Path, required=True, help="CRISPR detection results (JSON)")
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parser.add_argument("--toxin-results", type=Path, required=True, help="Toxin detection results (JSON or TXT)")
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parser.add_argument("--genome", type=Path, required=True, help="Original genome file (.fna)")
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parser.add_argument("--output", "-o", type=Path, required=True, help="Output analysis JSON")
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parser.add_argument("--mock", action="store_true", help="Use mock analysis logic")
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return parser.parse_args()
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def load_json(path: Path) -> Dict:
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with open(path) as f:
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return json.load(f)
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def calculate_distance(range1: str, range2: str) -> int:
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"""
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Calculate distance between two genomic ranges.
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Format: 'contig:start-end'
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"""
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try:
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contig1, coords1 = range1.split(':')
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start1, end1 = map(int, coords1.split('-'))
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contig2, coords2 = range2.split(':')
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start2, end2 = map(int, coords2.split('-'))
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if contig1 != contig2:
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return -1 # Different contigs
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# Check for overlap
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if max(start1, start2) <= min(end1, end2):
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return 0
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# Calculate distance
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if start1 > end2:
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return start1 - end2
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else:
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return start2 - end1
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except Exception as e:
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logger.warning(f"Error calculating distance: {e}")
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return -1
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def mock_blast_spacers(spacers: List[str], toxins: List[Dict]) -> List[Dict]:
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"""Mock BLAST spacers against toxins"""
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matches = []
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# Simulate a match if 'Cry' is in the spacer name (just for demo logic) or random
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# In reality, we'd blast sequences.
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# Let's just create a fake match for the first spacer
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if spacers and toxins:
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matches.append({
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"spacer_seq": spacers[0],
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"target_toxin": toxins[0].get("name", "Unknown"),
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"identity": 98.5,
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"alignment_length": 32,
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"mismatches": 1
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})
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return matches
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def perform_fusion_analysis(crispr_data: Dict, toxin_file: Path, mock: bool = False) -> Dict:
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"""
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Main analysis logic.
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1. Map CRISPR arrays
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2. Map Toxin genes
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3. Calculate distances
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4. Check for spacer matches
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"""
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analysis_results = {
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"strain_id": crispr_data.get("strain_id"),
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"associations": [],
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"summary": {"proximal_pairs": 0, "spacer_matches": 0}
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}
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# Extract arrays
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arrays = crispr_data.get("arrays", [])
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# Mock Toxin Parsing (assuming simple list for now if not JSON)
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toxins = []
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if mock:
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toxins = [
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{"name": "Cry1Ac1", "position": "contig_1:10000-12000"},
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{"name": "Vip3Aa1", "position": "contig_2:60000-62000"}
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]
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else:
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# TODO: Implement real toxin file parsing (e.g. from All_Toxins.txt)
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logger.warning("Real toxin parsing not implemented yet, using empty list")
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# Analyze Proximity
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for array in arrays:
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array_pos = f"{array.get('contig')}:{array.get('start')}-{array.get('end')}"
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for toxin in toxins:
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dist = calculate_distance(array_pos, toxin["position"])
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if dist != -1 and dist < 10000: # 10kb window
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association = {
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"type": "proximity",
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"array_id": array.get("id"),
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"toxin": toxin["name"],
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"distance": dist,
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"array_position": array_pos,
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"toxin_position": toxin["position"]
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}
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analysis_results["associations"].append(association)
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analysis_results["summary"]["proximal_pairs"] += 1
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# Analyze Spacer Matches (Mock)
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all_spacers = []
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for array in arrays:
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for spacer in array.get("spacers", []):
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all_spacers.append(spacer.get("sequence"))
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matches = mock_blast_spacers(all_spacers, toxins)
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for match in matches:
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analysis_results["associations"].append({
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"type": "spacer_match",
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**match
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})
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analysis_results["summary"]["spacer_matches"] += 1
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return analysis_results
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def main():
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args = parse_args()
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if not args.crispr_results.exists():
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logger.error(f"CRISPR results file not found: {args.crispr_results}")
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sys.exit(1)
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try:
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crispr_data = load_json(args.crispr_results)
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results = perform_fusion_analysis(crispr_data, args.toxin_results, args.mock)
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# Write results
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with open(args.output, 'w') as f:
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json.dump(results, f, indent=2)
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logger.info(f"Fusion analysis complete. Results: {args.output}")
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except Exception as e:
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logger.error(f"Error during fusion analysis: {e}")
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sys.exit(1)
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if __name__ == "__main__":
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main()
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