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| author | Frederick Muriuki Muriithi | 2024-01-04 01:28:58 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-04 01:28:58 +0300 |
| commit | 0f1dda20ea48f0fa411ff63f86b7e4b9c07e7c99 (patch) | |
| tree | a7e76c45e6bea53f2322ccbdf47383131ab627d7 /tests/r_qtl/test_r_qtl2_map_files.py | |
| parent | 3e51fb24fd34bab2164a5f4056bc78d21827ca29 (diff) | |
| download | gn-uploader-0f1dda20ea48f0fa411ff63f86b7e4b9c07e7c99.tar.gz | |
Rename test module.
Diffstat (limited to 'tests/r_qtl/test_r_qtl2_map_files.py')
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_map_files.py | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/tests/r_qtl/test_r_qtl2_map_files.py b/tests/r_qtl/test_r_qtl2_map_files.py new file mode 100644 index 0000000..5c8ca6a --- /dev/null +++ b/tests/r_qtl/test_r_qtl2_map_files.py @@ -0,0 +1,48 @@ +"""Test the parsing of the R/qtl2 gmap 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,mapfiletype,expected", + (("tests/r_qtl/test_files/test_gmap.zip", + "gmap", + ({"marker": "PVV4", "chr": "1", "pos": "0.000000"}, + {"marker": "AXR-1", "chr": "1", "pos": "6.250674"}, + {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"}, + {"marker": "EC.480C", "chr": "1", "pos": "12.577629"}, + {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})), + ("tests/r_qtl/test_files/test_gmap_transposed.zip", + "gmap", + ({"marker": "PVV4", "chr": "1", "pos": "0.000000"}, + {"marker": "AXR-1", "chr": "1", "pos": "6.250674"}, + {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"}, + {"marker": "EC.480C", "chr": "1", "pos": "12.577629"}, + {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})), + ("tests/r_qtl/test_files/test_pmap.zip", + "pmap", + ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"}, + {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"}, + {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"}, + {"marker": "D2Mit379", "chr": "2", "pos": "37.451062"}, + {"marker": "D2Mit75", "chr": "2", "pos": "80.584782"})), + ("tests/r_qtl/test_files/test_pmap_transposed.zip", + "pmap", + ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"}, + {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"}, + {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"}, + {"marker": "D2Mit379", "chr": "2", "pos": "37.451062"}, + {"marker": "D2Mit75", "chr": "2", "pos": "80.584782"})))) +def test_parse_map_files(relpath, mapfiletype, expected): + """ + GIVEN: A path to a zip file, `relpath` and the type of the map file, + WHEN: we parse the R/qtl2 map file, + THEN: ensure the parsed data is as expected. + """ + with ZipFile(Path(relpath).absolute(), "r") as zfile: + cdata = rqtl2.control_data(zfile) + assert tuple(rqtl2.file_data(zfile, mapfiletype, cdata)) == expected |