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-rw-r--r--tests/r_qtl/test_r_qtl2_covar.py36
1 files changed, 36 insertions, 0 deletions
diff --git a/tests/r_qtl/test_r_qtl2_covar.py b/tests/r_qtl/test_r_qtl2_covar.py
new file mode 100644
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--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_covar.py
@@ -0,0 +1,36 @@
+"""Test parsing of 'covar' 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