From 1c847583e22b47c7b51632c13a4e2fc18e90e02b Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 4 Jan 2024 02:18:58 +0300
Subject: Add tests for parsing cross information (covar) files.

---
 tests/r_qtl/test_files/test_covar.zip            | Bin 0 -> 490 bytes
 tests/r_qtl/test_files/test_covar_transposed.zip | Bin 0 -> 541 bytes
 tests/r_qtl/test_r_qtl2_cross_information.py     |  36 +++++++++++++++++++++++
 3 files changed, 36 insertions(+)
 create mode 100644 tests/r_qtl/test_files/test_covar.zip
 create mode 100644 tests/r_qtl/test_files/test_covar_transposed.zip
 create mode 100644 tests/r_qtl/test_r_qtl2_cross_information.py

(limited to 'tests')

diff --git a/tests/r_qtl/test_files/test_covar.zip b/tests/r_qtl/test_files/test_covar.zip
new file mode 100644
index 0000000..6fbb5e9
Binary files /dev/null and b/tests/r_qtl/test_files/test_covar.zip differ
diff --git a/tests/r_qtl/test_files/test_covar_transposed.zip b/tests/r_qtl/test_files/test_covar_transposed.zip
new file mode 100644
index 0000000..5e933cc
Binary files /dev/null and b/tests/r_qtl/test_files/test_covar_transposed.zip differ
diff --git a/tests/r_qtl/test_r_qtl2_cross_information.py b/tests/r_qtl/test_r_qtl2_cross_information.py
new file mode 100644
index 0000000..f004fd3
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_cross_information.py
@@ -0,0 +1,36 @@
+"""Test parsing of cross-information files."""
+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_covar.zip",
+      ({"id": "1", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "2", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "3", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "146", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "147", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "148", "sex": "f", "cross_direction": "(BxS)x(BxS)"})),
+     ("tests/r_qtl/test_files/test_covar_transposed.zip",
+      ({"id": "1", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "2", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "3", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "146", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "147", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
+       {"id": "148", "sex": "f", "cross_direction": "(BxS)x(BxS)"})),
+     ))
+def test_parse_covar_files(filepath, expected):
+    """Test parsing of 'covar' files from the R/qtl2 bundle.
+
+    GIVEN: path to a R/qtl2 bundle
+    WHEN: the 'covar' file is parsed
+    THEN: verify the parsed data is as expected
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        cdata = rqtl2.control_data(zfile)
+        assert tuple(rqtl2.file_data(zfile, "covar", cdata)) == expected
-- 
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