diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_parse_multiple.py | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/tests/r_qtl/test_r_qtl2_parse_multiple.py b/tests/r_qtl/test_r_qtl2_parse_multiple.py new file mode 100644 index 0000000..c4c8ccb --- /dev/null +++ b/tests/r_qtl/test_r_qtl2_parse_multiple.py @@ -0,0 +1,57 @@ +"""Test the parsing of the R/qtl2 bundles with multiple values for file keys.""" +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,filekey,expected", + (("tests/r_qtl/test_files/test_geno_multiple.zip", + "geno", + ({ + "id": "1", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1, + "EC.66C": 1 + }, { + "id": "2", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1, + "EC.66C": 1 + }, { + "id": "3", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": None, + "EC.480C": 1, "EC.66C": 1 + }, { + "id": "4", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1, + "EC.66C": 1 + }, { + "id": "5", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2, + "EC.66C": 2 + }, { + "id": "6", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2, + "EC.66C": 2 + }, { + "id": "7", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1, + "EC.66C": 1 + }, { + "id": "8", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 1, + "EC.66C": 1 + }, { + "id": "9", "PVV4": None, "AXR-1": 2, "HH.335C-Col/PhyA": 2, + "EC.480C": 2, "EC.66C": 2 + }, { + "id": "10", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2, + "EC.66C": 2 + })),)) +def test_parse_multiple_files(filepath, filekey, expected): + """Test parsing of files from R/qtl2 bundle where file keys have multiple values. + + GIVEN: Path to a zip file with R/qtl2 data + WHEN: we parse the geno file + THEN: ensure that the data we get is as expected + """ + with ZipFile(Path(filepath).absolute(), "r") as zfile: + cdata = rqtl2.control_data(zfile) + process_fns = (rqtl2.make_process_data_geno(cdata) + if filekey == "geno" else tuple()) + assert tuple(rqtl2.file_data( + zfile, filekey, cdata, *process_fns)) == expected |