feat(crispr): implement CRISPR-Cas detection and fusion analysis module

crispr_cas/tests/test_detect_crispr.py

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+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"