diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/r_qtl/test_files/test_pmap.zip | bin | 0 -> 531 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_files/test_pmap_transposed.zip | bin | 0 -> 583 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2.py | 43 |
3 files changed, 22 insertions, 21 deletions
diff --git a/tests/r_qtl/test_files/test_pmap.zip b/tests/r_qtl/test_files/test_pmap.zip new file mode 100644 index 0000000..a3fadd5 --- /dev/null +++ b/tests/r_qtl/test_files/test_pmap.zip Binary files differdiff --git a/tests/r_qtl/test_files/test_pmap_transposed.zip b/tests/r_qtl/test_files/test_pmap_transposed.zip new file mode 100644 index 0000000..5d9f51b --- /dev/null +++ b/tests/r_qtl/test_files/test_pmap_transposed.zip Binary files differdiff --git a/tests/r_qtl/test_r_qtl2.py b/tests/r_qtl/test_r_qtl2.py index a72b300..33ff5e5 100644 --- a/tests/r_qtl/test_r_qtl2.py +++ b/tests/r_qtl/test_r_qtl2.py @@ -8,40 +8,41 @@ from r_qtl import r_qtl2 as rqtl2 @pytest.mark.unit_test @pytest.mark.parametrize( - "relpath,expected", + "relpath,mapfiletype,expected", (("tests/r_qtl/test_files/test_gmap.zip", + "genetic-map", ({"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", + "genetic-map", ({"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"})))) -def test_parse_gmap_files(relpath, expected): + {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})), + ("tests/r_qtl/test_files/test_pmap.zip", + "physical-map", + ({"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", + "physical-map", + ({"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` - WHEN: we parse a gmap file + 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: assert rqtl2.map_data( - zfile, "genetic-map", rqtl2.control_data(zfile)) == expected - -@pytest.mark.skip(reason="Test not implemented yet.") -@pytest.mark.unit_test -@pytest.mark.parametrize( - "relpath,expected", - (("tests/r_qtl/test_files/test_pmap.zip", - ()), - ("tests/r_qtl/test_files/test_pmap_transposed.zip", - ()))) -def test_parse_pmap_files(relpath, expected): - """ - GIVEN: A path to a zip file, `relpath` - WHEN: we parse a pmap file - THEN: ensure the parsed data is as expected. - """ + zfile, mapfiletype, rqtl2.control_data(zfile)) == expected |