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>

tools/crispr_cas_analysis/pixi.toml

@@ -0,0 +1,30 @@
+[workspace]
+authors = ["zly <644706215@qq.com>"]
+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"]
+name = "crispr_cas_analysis"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[dependencies]
+python = ">=3.10"
+wget = "*"
+curl = "*"
+git = "*"
+java-jdk = "*"
+parallel = "*"
+perl-app-cpanminus = "*"
+hmmer = "*"
+emboss = "*"
+blast = "*"
+perl-bioperl-core = "*"
+perl-xml-simple = "*"
+perl-digest-md5 = "*"
+vmatch = "*"
+muscle = "*"
+prodigal = "*"
+mamba = "*"
+macsyfinder = "==2.1.2"
+
+[tasks]
+install-casfinder = "macsydata install -u CASFinder==3.1.0"
+detect = "python scripts/detect_crispr.py"

tools/crispr_cas_analysis/tests/__init__.py

@@ -1 +0,0 @@
-"""Tests for CRISPR-Cas module"""

tools/crispr_cas_analysis/tests/test_detect_crispr.py

@@ -1,42 +0,0 @@
-import pytest
-import json
-import shutil
-from pathlib import Path
-from crispr_cas.scripts.detect_crispr import generate_mock_results
-
-def test_generate_mock_results(tmp_path):
-    """Test mock result generation"""
-    input_file = tmp_path / "test_genome.fna"
-    input_file.touch()
-
-    results = generate_mock_results(input_file)
-
-    assert results["strain_id"] == "test_genome"
-    assert "cas_systems" in results
-    assert "arrays" in results
-    assert results["summary"]["has_cas"] is True
-    assert len(results["arrays"]) > 0
-
-def test_script_execution(tmp_path):
-    """Test full script execution via subprocess"""
-    # Create dummy input
-    input_file = tmp_path / "genome.fna"
-    input_file.touch()
-    output_file = tmp_path / "results.json"
-    script_path = Path("crispr_cas/scripts/detect_crispr.py").absolute()
-
-    import subprocess
-    cmd = [
-        "python3", str(script_path),
-        "--input", str(input_file),
-        "--output", str(output_file),
-        "--mock"
-    ]
-
-    result = subprocess.run(cmd, capture_output=True, text=True)
-    assert result.returncode == 0
-    assert output_file.exists()
-
-    with open(output_file) as f:
-        data = json.load(f)
-        assert data["strain_id"] == "genome"

tools/crispr_cas_analysis/tests/test_fusion_analysis.py

@@ -1,93 +0,0 @@
-import pytest
-import json
-from pathlib import Path
-import sys
-
-# Add project root to path to allow importing modules
-sys.path.insert(0, str(Path(__file__).parents[2]))
-
-from crispr_cas.scripts.fusion_analysis import calculate_distance, perform_fusion_analysis
-
-def test_calculate_distance():
-    """Test genomic distance calculation"""
-    # Same contig, no overlap
-    # Range1: 100-200, Range2: 300-400 -> Dist 100
-    assert calculate_distance("c1:100-200", "c1:300-400") == 100
-
-    # Same contig, overlap
-    # Range1: 100-300, Range2: 200-400 -> Dist 0
-    assert calculate_distance("c1:100-300", "c1:200-400") == 0
-
-    # Different contig
-    assert calculate_distance("c1:100-200", "c2:300-400") == -1
-
-    # Invalid format
-    assert calculate_distance("invalid", "c1:100-200") == -1
-
-def test_fusion_analysis_logic(tmp_path):
-    """Test main analysis logic with mock data"""
-
-    # Mock CRISPR data
-    crispr_data = {
-        "strain_id": "test_strain",
-        "arrays": [
-            {
-                "id": "A1",
-                "contig": "contig_1",
-                "start": 1000,
-                "end": 2000,
-                "spacers": [{"sequence": "ATGC"}]
-            }
-        ]
-    }
-
-    # Mock toxin file (just a placeholder for path)
-    toxin_file = tmp_path / "toxins.txt"
-    toxin_file.touch()
-
-    # Run analysis in mock mode
-    # In mock mode, the script generates its own toxin list:
-    # {"name": "Cry1Ac1", "position": "contig_1:10000-12000"}
-    # Distance: 10000 - 2000 = 8000 (< 10000 threshold) -> Should match
-
-    results = perform_fusion_analysis(crispr_data, toxin_file, mock=True)
-
-    assert results["strain_id"] == "test_strain"
-    assert len(results["associations"]) > 0
-
-    # Check for proximity match
-    proximity_matches = [a for a in results["associations"] if a["type"] == "proximity"]
-    assert len(proximity_matches) > 0
-    assert proximity_matches[0]["distance"] == 8000
-
-def test_script_execution(tmp_path):
-    """Test full script execution via subprocess"""
-
-    # Create input files
-    crispr_file = tmp_path / "crispr.json"
-    with open(crispr_file, 'w') as f:
-        json.dump({"strain_id": "test", "arrays": []}, f)
-
-    toxin_file = tmp_path / "toxins.txt"
-    toxin_file.touch()
-
-    genome_file = tmp_path / "genome.fna"
-    genome_file.touch()
-
-    output_file = tmp_path / "output.json"
-
-    script_path = Path("crispr_cas/scripts/fusion_analysis.py").absolute()
-
-    import subprocess
-    cmd = [
-        "python3", str(script_path),
-        "--crispr-results", str(crispr_file),
-        "--toxin-results", str(toxin_file),
-        "--genome", str(genome_file),
-        "--output", str(output_file),
-        "--mock"
-    ]
-
-    result = subprocess.run(cmd, capture_output=True, text=True)
-    assert result.returncode == 0
-    assert output_file.exists()