Parse the phenotype data from the R/qtl2 bundle.

3 files changed, 33 insertions, 0 deletions

diff --git a/tests/r_qtl/test_files/test_pheno.zip b/tests/r_qtl/test_files/test_pheno.zip
new file mode 100644
index 0000000..5c709e7
--- /dev/null
+++ b/tests/r_qtl/test_files/test_pheno.zip
diff --git a/tests/r_qtl/test_files/test_pheno_transposed.zip b/tests/r_qtl/test_files/test_pheno_transposed.zip
new file mode 100644
index 0000000..9bff030
--- /dev/null
+++ b/tests/r_qtl/test_files/test_pheno_transposed.zip
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
new file mode 100644
index 0000000..554d9c8
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -0,0 +1,33 @@
+"""Test parsing of pheno files in a R/qtl2 bundle."""
+from pathlib import Path
+
+import pytest
+from zipfile import ZipFile
+
+from r_qtl import r_qtl2 as rqtl2
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/test_pheno.zip",
+      ({"id": "1", "liver": "61.92", "spleen": "153.16"},
+       {"id": "2", "liver": "88.33", "spleen": "178.58"},
+       {"id": "3", "liver": "58", "spleen": "131.91"},
+       {"id": "4", "liver": "78.06", "spleen": "126.13"},
+       {"id": "5", "liver": "65.31", "spleen": "181.05"})),
+     ("tests/r_qtl/test_files/test_pheno_transposed.zip",
+      ({"id": "1", "liver": "61.92", "spleen": "153.16"},
+       {"id": "2", "liver": "88.33", "spleen": "178.58"},
+       {"id": "3", "liver": "58", "spleen": "131.91"},
+       {"id": "4", "liver": "78.06", "spleen": "126.13"},
+       {"id": "5", "liver": "65.31", "spleen": "181.05"}))))
+def test_parse_pheno_files(filepath, expected):
+    """Test parsing of 'pheno' files from the R/qtl2 bundle.
+
+    GIVEN: path to a R/qtl2 bundle
+    WHEN: the 'pheno' file is parsed
+    THEN: verify the parsed data is as expected
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        assert tuple(
+            rqtl2.phenotype_data(zfile, rqtl2.control_data(zfile))) == expected