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| author | Frederick Muriuki Muriithi | 2024-01-04 02:18:58 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-04 02:18:58 +0300 |
| commit | 1c847583e22b47c7b51632c13a4e2fc18e90e02b (patch) | |
| tree | a68082aa2d48aa43f35fbeb9981cb0eb69a8bb02 | |
| parent | e587f67c73866d4edbf90e1a44b11074912df600 (diff) | |
| download | gn-uploader-1c847583e22b47c7b51632c13a4e2fc18e90e02b.tar.gz | |
Add tests for parsing cross information (covar) files.
| -rw-r--r-- | tests/r_qtl/test_files/test_covar.zip | bin | 0 -> 490 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_files/test_covar_transposed.zip | bin | 0 -> 541 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_cross_information.py | 36 |
3 files changed, 36 insertions, 0 deletions
diff --git a/tests/r_qtl/test_files/test_covar.zip b/tests/r_qtl/test_files/test_covar.zip Binary files differnew file mode 100644 index 0000000..6fbb5e9 --- /dev/null +++ b/tests/r_qtl/test_files/test_covar.zip diff --git a/tests/r_qtl/test_files/test_covar_transposed.zip b/tests/r_qtl/test_files/test_covar_transposed.zip Binary files differnew file mode 100644 index 0000000..5e933cc --- /dev/null +++ b/tests/r_qtl/test_files/test_covar_transposed.zip 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 |