From 5f5cc8503ec10319ee4d9e7d6bd739cc6190561c Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 4 Jan 2024 17:35:48 +0300
Subject: Parse sex information from R/qtl bundle.

---
 tests/r_qtl/test_files/test_cross_info_01.zip | Bin 597 -> 594 bytes
 tests/r_qtl/test_files/test_cross_info_02.zip | Bin 778 -> 775 bytes
 tests/r_qtl/test_files/test_sex_info_01.zip   | Bin 0 -> 589 bytes
 tests/r_qtl/test_files/test_sex_info_02.zip   | Bin 0 -> 773 bytes
 tests/r_qtl/test_r_qtl2_sex_information.py    |  35 ++++++++++++++++++++++++++
 5 files changed, 35 insertions(+)
 create mode 100644 tests/r_qtl/test_files/test_sex_info_01.zip
 create mode 100644 tests/r_qtl/test_files/test_sex_info_02.zip
 create mode 100644 tests/r_qtl/test_r_qtl2_sex_information.py

(limited to 'tests')

diff --git a/tests/r_qtl/test_files/test_cross_info_01.zip b/tests/r_qtl/test_files/test_cross_info_01.zip
index 1211f96..6143a9f 100644
Binary files a/tests/r_qtl/test_files/test_cross_info_01.zip and b/tests/r_qtl/test_files/test_cross_info_01.zip differ
diff --git a/tests/r_qtl/test_files/test_cross_info_02.zip b/tests/r_qtl/test_files/test_cross_info_02.zip
index dddd281..7e23fc4 100644
Binary files a/tests/r_qtl/test_files/test_cross_info_02.zip and b/tests/r_qtl/test_files/test_cross_info_02.zip differ
diff --git a/tests/r_qtl/test_files/test_sex_info_01.zip b/tests/r_qtl/test_files/test_sex_info_01.zip
new file mode 100644
index 0000000..bc60d84
Binary files /dev/null and b/tests/r_qtl/test_files/test_sex_info_01.zip differ
diff --git a/tests/r_qtl/test_files/test_sex_info_02.zip b/tests/r_qtl/test_files/test_sex_info_02.zip
new file mode 100644
index 0000000..c862b73
Binary files /dev/null and b/tests/r_qtl/test_files/test_sex_info_02.zip differ
diff --git a/tests/r_qtl/test_r_qtl2_sex_information.py b/tests/r_qtl/test_r_qtl2_sex_information.py
new file mode 100644
index 0000000..90eae8d
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_sex_information.py
@@ -0,0 +1,35 @@
+"""Test loading of sex information."""
+
+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_sex_info_01.zip",
+      ({"id": "1", "sex": "male"},
+       {"id": "2", "sex": "male"},
+       {"id": "3", "sex": "male"},
+       {"id": "71", "sex": "male"},
+       {"id": "72", "sex": "male"},
+       {"id": "146", "sex": "female"},
+       {"id": "147", "sex": "female"},
+       {"id": "148", "sex": "female"})),
+     ("tests/r_qtl/test_files/test_sex_info_02.zip",
+      ({"id": "1", "sex": "male"},
+       {"id": "2", "sex": "male"},
+       {"id": "3", "sex": "male"},
+       {"id": "71", "sex": "male"},
+       {"id": "72", "sex": "male"},
+       {"id": "146", "sex": "female"},
+       {"id": "147", "sex": "female"},
+       {"id": "148", "sex": "female"}))))
+def test_parse_sex_info(filepath, expected):
+    """Test parsing of sex information."""
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        assert tuple(rqtl2.sex_information(
+            zfile, rqtl2.control_data(zfile))) == expected
-- 
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