add CRISPR PILER-CR test

test/test_crispr.py

@@ -0,0 +1,48 @@
+import json
+
+from pathlib import Path
+from subprocess import run
+
+import bakta.config as cfg
+
+import pytest
+
+CRISPR_ARRAYS = [
+    {
+        'repeat_consensus': 'CGGTTTATCCCCGCTGGCGCGGGGAACACA',
+        'spacers': [
+            'AACCGAAACACACGATCAATCCGAATATGAG',
+            'TTGGTGACAGTTTTTGTCACTGTTTTGGTGA',
+            'CTAAGCATACATATCTGTTTTTAAACA'
+        ],
+        'repeats': 3
+    }
+]
+
+
+
+
+def test_crispr_arrays(tmpdir):
+    proc = run(
+        [
+            'bin/bakta', '--db', 'test/db', '--output', tmpdir, '--force', '--prefix', 'test',
+            '--skip-tmrna', '--skip-trna', '--skip-rrna', '--skip-ncrna', '--skip-ncrna-region', '--skip-cds', '--skip-sorf', '--skip-ori', '--skip-gap', '--skip-plot',
+            'test/data/GCF_000008865.2.fna.gz'
+        ]
+    )
+    assert proc.returncode == 0
+
+    results_path = Path(tmpdir).joinpath('test.json')
+    assert Path.exists(results_path)
+
+    results = None
+    with results_path.open() as fh:
+        results = json.load(fh)
+    assert results is not None
+
+    crispr_arrays = [feat for feat in results['features'] if feat['type'] == 'crispr']
+    assert len(crispr_arrays) == 1
+
+    for idx, crispr_array in enumerate(crispr_arrays):
+        assert crispr_array['repeat_consensus'] == CRISPR_ARRAYS[idx]['repeat_consensus']
+        assert len(crispr_array['repeats']) == CRISPR_ARRAYS[idx]['repeats']