Added tests for ShigaPass

tests/fixtures/__init__.py

@@ -1,5 +1,6 @@
 """Fixtures"""
 
 from .ecoli import *
+from .shigella import *
 from .saureus import *
 from .mtuberculosis import *

tests/fixtures/shigella/__init__.py

@@ -0,0 +1,9 @@
+"""Fixtures for Shigella."""
+import pytest
+
+from ..fixtures import data_path
+
+@pytest.fixture()
+def shigella_shigapass_path(data_path):
+    """Get path for Shigapass results for shigella."""
+    return str(data_path.joinpath("shigella", "shigapass.csv"))

tests/fixtures/shigella/shigapass.csv

@@ -0,0 +1,5 @@
+Name;rfb;rfb_hits,(%);MLST;fliC;CRISPR;ipaH;Predicted_Serotype;Predicted_FlexSerotype;Comments
+ERR5888634;C2;79,(48.2%);ST145;ShH57(ShH3cplx);A-var2;ipaH+;SB2;;
+ERR5952732;B1-5;139,(93.3%);ST245;ShH2(ShH2cplx);A-var3,x,16;ipaH+;SF1-5;1b;
+ERR5976293;D;202,(70.6%);ST152;ShH25(ShH1cplx);A-var0,27;ipaH+;SS;;
+ERR5982186;A2;100,(61.7%);ST147;none;A-var1,12,3,5,11-var1;ipaH+;SD2;;

tests/parse/test_shigapass.py

@@ -0,0 +1,69 @@
+"""Test functions for parsing Shigapass results."""
+
+import pytest
+from prp.parse.phenotype.shigapass import parse_shigapass_pred, _extract_percentage
+
+
+@pytest.mark.parametrize(
+    "input,expected",
+    [
+        ("79,(48.2%)", 48.2),
+        ("79,(48.0%)", 48.0),
+        ("79,(48%)", 48.0),
+        ("NA,(0.0%)", 0.0),
+        ("NA,(0%)", 0.0),
+    ],
+)
+def test_extract_percentage(input, expected):
+    """
+    Test that the percentage can be extracted from rfb_hits.
+
+    "foo, (12%)" -> 12%
+    """
+    result = _extract_percentage(input)
+    assert result == expected
+
+
+def test_parse_shigapass_results(ecoli_shigapass_path, shigella_shigapass_path):
+    """Test parsing of shigapass result files."""
+
+    # test parsing the output of an ecoli.
+    result = parse_shigapass_pred(ecoli_shigapass_path)
+    expected_ecoli = {
+        "type": "shigatype",
+        "software": "shigapass",
+        "result": {
+            "rfb": None,
+            "rfb_hits": 0.0,
+            "mlst": None,
+            "flic": None,
+            "crispr": None,
+            "ipah": "ipaH-",
+            "predicted_serotype": "Not Shigella/EIEC",
+            "predicted_flex_serotype": None,
+            "comments": None,
+        },
+    }
+    # check if data matches
+    assert expected_ecoli == result[0].model_dump()
+
+    # test parsing the output with a shigella.
+    result = parse_shigapass_pred(shigella_shigapass_path)
+    expected_shigella = {
+        "type": "shigatype",
+        "software": "shigapass",
+        "result": {
+            "rfb": "C2",
+            "rfb_hits": 48.2,
+            "mlst": "ST145",
+            "flic": "ShH57(ShH3cplx)",
+            "crispr": "A-var2",
+            "ipah": "ipaH+",
+            "predicted_serotype": "SB2",
+            "predicted_flex_serotype": None,
+            "comments": None,
+        },
+    }
+
+    # check if data matches
+    assert expected_shigella == result[0].model_dump()