Fix(pipeline): prevent nested zip packaging and update CRISPR dependencies
- Add filter to skip .zip and .tar.gz files when creating result archive - Update CRISPR feature with CASFinder dependencies (hmmer, blast, vmatch, etc.) - Add install-casfinder task for macsydata installation - Remove obsolete CRISPR test files Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
zly
30
tools/crispr_cas_analysis/pixi.toml
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30
tools/crispr_cas_analysis/pixi.toml
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[workspace]
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authors = ["zly <644706215@qq.com>"]
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channels = ["https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge", "https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda", "https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main"]
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name = "crispr_cas_analysis"
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platforms = ["linux-64"]
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version = "0.1.0"
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[dependencies]
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python = ">=3.10"
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wget = "*"
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curl = "*"
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git = "*"
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java-jdk = "*"
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parallel = "*"
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perl-app-cpanminus = "*"
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hmmer = "*"
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emboss = "*"
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blast = "*"
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perl-bioperl-core = "*"
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perl-xml-simple = "*"
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perl-digest-md5 = "*"
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vmatch = "*"
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muscle = "*"
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prodigal = "*"
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mamba = "*"
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macsyfinder = "==2.1.2"
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[tasks]
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install-casfinder = "macsydata install -u CASFinder==3.1.0"
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detect = "python scripts/detect_crispr.py"
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"""Tests for CRISPR-Cas module"""
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import pytest
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import json
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import shutil
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from pathlib import Path
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from crispr_cas.scripts.detect_crispr import generate_mock_results
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def test_generate_mock_results(tmp_path):
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"""Test mock result generation"""
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input_file = tmp_path / "test_genome.fna"
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input_file.touch()
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results = generate_mock_results(input_file)
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assert results["strain_id"] == "test_genome"
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assert "cas_systems" in results
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assert "arrays" in results
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assert results["summary"]["has_cas"] is True
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assert len(results["arrays"]) > 0
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def test_script_execution(tmp_path):
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"""Test full script execution via subprocess"""
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# Create dummy input
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input_file = tmp_path / "genome.fna"
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input_file.touch()
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output_file = tmp_path / "results.json"
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script_path = Path("crispr_cas/scripts/detect_crispr.py").absolute()
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import subprocess
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cmd = [
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"python3", str(script_path),
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"--input", str(input_file),
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"--output", str(output_file),
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"--mock"
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]
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result = subprocess.run(cmd, capture_output=True, text=True)
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assert result.returncode == 0
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assert output_file.exists()
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with open(output_file) as f:
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data = json.load(f)
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assert data["strain_id"] == "genome"
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@@ -1,93 +0,0 @@
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import pytest
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import json
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from pathlib import Path
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import sys
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# Add project root to path to allow importing modules
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sys.path.insert(0, str(Path(__file__).parents[2]))
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from crispr_cas.scripts.fusion_analysis import calculate_distance, perform_fusion_analysis
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def test_calculate_distance():
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"""Test genomic distance calculation"""
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# Same contig, no overlap
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# Range1: 100-200, Range2: 300-400 -> Dist 100
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assert calculate_distance("c1:100-200", "c1:300-400") == 100
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# Same contig, overlap
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# Range1: 100-300, Range2: 200-400 -> Dist 0
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assert calculate_distance("c1:100-300", "c1:200-400") == 0
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# Different contig
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assert calculate_distance("c1:100-200", "c2:300-400") == -1
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# Invalid format
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assert calculate_distance("invalid", "c1:100-200") == -1
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def test_fusion_analysis_logic(tmp_path):
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"""Test main analysis logic with mock data"""
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# Mock CRISPR data
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crispr_data = {
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"strain_id": "test_strain",
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"arrays": [
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{
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"id": "A1",
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"contig": "contig_1",
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"start": 1000,
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"end": 2000,
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"spacers": [{"sequence": "ATGC"}]
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}
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]
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}
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# Mock toxin file (just a placeholder for path)
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toxin_file = tmp_path / "toxins.txt"
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toxin_file.touch()
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# Run analysis in mock mode
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# In mock mode, the script generates its own toxin list:
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# {"name": "Cry1Ac1", "position": "contig_1:10000-12000"}
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# Distance: 10000 - 2000 = 8000 (< 10000 threshold) -> Should match
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results = perform_fusion_analysis(crispr_data, toxin_file, mock=True)
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assert results["strain_id"] == "test_strain"
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assert len(results["associations"]) > 0
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# Check for proximity match
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proximity_matches = [a for a in results["associations"] if a["type"] == "proximity"]
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assert len(proximity_matches) > 0
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assert proximity_matches[0]["distance"] == 8000
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def test_script_execution(tmp_path):
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"""Test full script execution via subprocess"""
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# Create input files
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crispr_file = tmp_path / "crispr.json"
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with open(crispr_file, 'w') as f:
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json.dump({"strain_id": "test", "arrays": []}, f)
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toxin_file = tmp_path / "toxins.txt"
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toxin_file.touch()
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genome_file = tmp_path / "genome.fna"
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genome_file.touch()
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output_file = tmp_path / "output.json"
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script_path = Path("crispr_cas/scripts/fusion_analysis.py").absolute()
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import subprocess
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cmd = [
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"python3", str(script_path),
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"--crispr-results", str(crispr_file),
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"--toxin-results", str(toxin_file),
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"--genome", str(genome_file),
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"--output", str(output_file),
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"--mock"
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]
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result = subprocess.run(cmd, capture_output=True, text=True)
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assert result.returncode == 0
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assert output_file.exists()
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