diff options
Diffstat (limited to 'tests/r_qtl/test_r_qtl2_covar.py')
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_covar.py | 36 |
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 index 0000000..c18ee74 --- /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 |