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| author | Frederick Muriuki Muriithi | 2023-12-28 09:55:26 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2023-12-28 09:55:26 +0300 |
| commit | d4fff5fda2d9fe2b9730a7cffcc8f85b3a8eff17 (patch) | |
| tree | e41ee6ab21815800b3daf35ff1df2f823241e5ed /tests | |
| parent | c687f9460ca071c714cdc9cba62449b59b001de8 (diff) | |
| download | gn-uploader-d4fff5fda2d9fe2b9730a7cffcc8f85b3a8eff17.tar.gz | |
Handle transposed geno files.
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_geno.py | 134 |
1 files changed, 54 insertions, 80 deletions
diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py index 5ebb5a9..908ef55 100644 --- a/tests/r_qtl/test_r_qtl2_geno.py +++ b/tests/r_qtl/test_r_qtl2_geno.py @@ -92,86 +92,60 @@ from r_qtl import r_qtl2 as rqtl2 "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 - })))) + ({"id": "1", "PVV4": 1}, + {"id": "2", "PVV4": 1}, + {"id": "3", "PVV4": 2}, + {"id": "4", "PVV4": 1}, + {"id": "5", "PVV4": 2}, + {"id": "6", "PVV4": 2}, + {"id": "7", "PVV4": 1}, + {"id": "8", "PVV4": 2}, + {"id": "9", "PVV4": None}, + {"id": "10", "PVV4": 2}, + + {"id": "1", "AXR-1": 1}, + {"id": "2", "AXR-1": 1}, + {"id": "3", "AXR-1": 2}, + {"id": "4", "AXR-1": 1}, + {"id": "5", "AXR-1": 2}, + {"id": "6", "AXR-1": 2}, + {"id": "7", "AXR-1": 1}, + {"id": "8", "AXR-1": 2}, + {"id": "9", "AXR-1": 2}, + {"id": "10", "AXR-1": 2}, + + {"id": "1", "HH.335C-Col/PhyA": 1}, + {"id": "2", "HH.335C-Col/PhyA": 1}, + {"id": "3", "HH.335C-Col/PhyA": None}, + {"id": "4", "HH.335C-Col/PhyA": 1}, + {"id": "5", "HH.335C-Col/PhyA": 2}, + {"id": "6", "HH.335C-Col/PhyA": 2}, + {"id": "7", "HH.335C-Col/PhyA": 1}, + {"id": "8", "HH.335C-Col/PhyA": 2}, + {"id": "9", "HH.335C-Col/PhyA": 2}, + {"id": "10", "HH.335C-Col/PhyA": 2}, + + {"id": "1", "EC.480C": 1}, + {"id": "2", "EC.480C": 1}, + {"id": "3", "EC.480C": 1}, + {"id": "4", "EC.480C": 1}, + {"id": "5", "EC.480C": 2}, + {"id": "6", "EC.480C": 2}, + {"id": "7", "EC.480C": 1}, + {"id": "8", "EC.480C": 1}, + {"id": "9", "EC.480C": 2}, + {"id": "10", "EC.480C": 2}, + + {"id": "1","EC.66C": 1}, + {"id": "2", "EC.66C": 1}, + {"id": "3", "EC.66C": 1}, + {"id": "4", "EC.66C": 1}, + {"id": "5", "EC.66C": 2}, + {"id": "6", "EC.66C": 2}, + {"id": "7", "EC.66C": 1}, + {"id": "8", "EC.66C": 1}, + {"id": "9", "EC.66C": 2}, + {"id": "10", "EC.66C": 2})))) def test_parse_geno_files(relpath,expected): """ GIVEN: Path to a zip file with R/qtl2 data |