Add pytests for delly

CHANGELOG.md

@@ -5,6 +5,8 @@
  - Added `sequencing_run` and `lims_id` to output (bonsai input)
  - Added function for annotating delly variants intersecting with resistance targets
  - Added capability of handling empty dictionaries from serotypefinder output
+ - Added pytest for `prp annotate-delly`
+ - Added `pyyaml` to docker image
 
 ### Fixed
 

pyproject.toml

@@ -25,7 +25,8 @@ dependencies = [
     "pandas==2.1.3",
     "Biopython==1.83",
     "cyvcf2",
-    "pysam"
+    "pysam",
+    "pyyaml"
 ]
 
 [project.urls]

tests/fixtures/mtuberculosis/__init__.py

@@ -51,3 +51,18 @@ def mtuberculosis_snv_vcf_path(data_path):
 def mtuberculosis_sv_vcf_path(data_path):
     """Get path for mtuberculosis meta file"""
     return str(data_path.joinpath("mtuberculosis", "sv.vcf"))
+
+@pytest.fixture()
+def mtuberculosis_delly_bcf_path(data_path):
+    """Get path for mtuberculosis meta file"""
+    return str(data_path.joinpath("mtuberculosis", "delly.bcf"))
+
+@pytest.fixture()
+def converged_bed_path(data_path):
+    """Get path for mtuberculosis converged who fohm tbdb bgzipped bed file"""
+    return str(data_path.joinpath("mtuberculosis", "converged_who_fohm_tbdb.bed.gz"))
+
+@pytest.fixture()
+def annotated_delly_path(data_path):
+    """Get path for annotated delly vcf file"""
+    return str(data_path.joinpath("mtuberculosis", "annotated_delly.vcf"))

tests/test_cli.py

@@ -4,7 +4,7 @@
 
 from click.testing import CliRunner
 
-from prp.cli import create_bonsai_input, create_cdm_input
+from prp.cli import create_bonsai_input, create_cdm_input, annotate_delly
 
 
 def test_create_output_saureus(
@@ -160,6 +160,36 @@ def test_cdm_input_cmd(
             assert cmd_output == ecoli_cdm_input
 
 
+def test_annotate_delly(
+    mtuberculosis_delly_bcf_path, converged_bed_path, annotated_delly_path
+):
+    """Test command for annotating delly output."""
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        sample_id = "test_mtuberculosis_1"
+        output_fname = f"{sample_id}_annotated_delly.vcf"
+        result = runner.invoke(
+            annotate_delly,
+            [
+                "--vcf",
+                mtuberculosis_delly_bcf_path,
+                "--bed",
+                converged_bed_path,
+                "--output",
+                output_fname,
+            ],
+        )
+
+        # test successful execution of command
+        assert result.exit_code == 0
+
+        # test correct output format
+        with open(output_fname, "r", encoding="utf-8") as test_annotated_delly_output, \
+            open(annotated_delly_path, "r", encoding="utf-8") as annotated_delly_output:
+            test_contents = test_annotated_delly_output.read()
+            expected_contents = annotated_delly_output.read()
+            assert test_contents == expected_contents
+
 
 def test_create_output_mtuberculosis(
     mtuberculosis_analysis_meta_path,