diff options
| author | Frederick Muriuki Muriithi | 2023-12-27 12:12:33 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2023-12-27 12:14:53 +0300 |
| commit | c687f9460ca071c714cdc9cba62449b59b001de8 (patch) | |
| tree | 48ad3343cbea9dddaa0e374a38cd11cb38c26fe5 /tests/r_qtl/test_r_qtl2_geno.py | |
| parent | 3294adc11ada56046ff748c08b97faf0eeed11b2 (diff) | |
| download | gn-uploader-c687f9460ca071c714cdc9cba62449b59b001de8.tar.gz | |
Tests: Test parsing of non-transposed geno files.
Check that the parsing of non-transposed geno files.
Leave in failing test for transposed geno files.
Diffstat (limited to 'tests/r_qtl/test_r_qtl2_geno.py')
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_geno.py | 182 |
1 files changed, 182 insertions, 0 deletions
diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py new file mode 100644 index 0000000..5ebb5a9 --- /dev/null +++ b/tests/r_qtl/test_r_qtl2_geno.py @@ -0,0 +1,182 @@ +"""Test the parsing of the R/qtl2 geno 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( + "relpath,expected", + ( + ("tests/r_qtl/test_files/test_geno.zip", + ({ + "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 + })), + ("tests/r_qtl/test_files/test_geno_transposed.zip", + ({ + "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_geno_files(relpath,expected): + """ + 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(relpath).absolute(), "r") as zfile: + assert tuple(rqtl2.genotype_data(zfile, rqtl2.control_data(zfile))) == expected |