Ensure control file defaults are set up in code.

3 files changed, 38 insertions, 0 deletions

diff --git a/tests/r_qtl/test_files/empty_control_file_json.zip b/tests/r_qtl/test_files/empty_control_file_json.zip
new file mode 100644
index 0000000..94cab39
--- /dev/null
+++ b/tests/r_qtl/test_files/empty_control_file_json.zip
diff --git a/tests/r_qtl/test_files/empty_control_file_yaml.zip b/tests/r_qtl/test_files/empty_control_file_yaml.zip
new file mode 100644
index 0000000..daf607f
--- /dev/null
+++ b/tests/r_qtl/test_files/empty_control_file_yaml.zip
diff --git a/tests/r_qtl/test_r_qtl2_control_file.py b/tests/r_qtl/test_r_qtl2_control_file.py
new file mode 100644
index 0000000..316307d
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_control_file.py
@@ -0,0 +1,38 @@
+"""Test the parsing of control file"""
+from pathlib import Path
+
+import pytest
+from zipfile import ZipFile
+
+from r_qtl import r_qtl2 as rqtl2
+
+__DEFAULTS__ = {
+    "description": "Empty control file to test defaults",
+    "sep": ",",
+    "na.strings": ["NA"],
+    "comment.char": "#",
+    "geno_transposed": False,
+    "founder_geno_transposed": False,
+    "pheno_transposed": False,
+    "covar_transposed": False,
+    "phenocovar_transposed": False,
+    "gmap_transposed": False,
+    "pmap_transposed": False,
+    "phenose_transposed": False
+}
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/empty_control_file_yaml.zip",
+      __DEFAULTS__),
+     ("tests/r_qtl/test_files/empty_control_file_json.zip",
+      __DEFAULTS__)))
+def test_defaults_are_set(filepath, expected):
+    """
+    GIVEN: path to a R/qtl2 bundle with an empty control file
+    WHEN: the control data is parsed
+    THEN: ensure all the defaults are set up correctly
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        assert rqtl2.control_data(zfile) == expected