diff options
| -rw-r--r-- | r_qtl/r_qtl2.py | 31 | ||||
| -rw-r--r-- | tests/r_qtl/test_files/test_covar.zip | bin | 490 -> 562 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_files/test_covar_transposed.zip | bin | 541 -> 594 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_covar.py | 30 |
4 files changed, 48 insertions, 13 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 26e8c76..682542b 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -134,6 +134,37 @@ def make_process_data_geno(cdata) -> tuple[ for items in zip(ids, vals[1:])) return (__non_transposed__, __transposed__) +def make_process_data_covar(cdata) -> tuple[ + Callable[[dict], dict], + Callable[[str, tuple[str, ...], tuple[str, ...]], + tuple[dict, ...]]]: + """Build functions to process sex and cross information in covar files.""" + def replace_sex_code(val): + sex_info = cdata.get("sex", False) + if bool(sex_info): + return sex_info.get(val, val) + return val + def replace_cross_info(val): + cross_info = cdata.get("cross_info", False) + if bool(cross_info): + return cross_info.get(val, val) + return val + def non_transposed(row: dict) -> dict: + return { + key: thread_op(value, replace_sex_code, replace_cross_info) + for key,value in row.items() + } + def transposed(id_key: str, + ids: tuple[str, ...], + vals: tuple[str, ...]) -> tuple[dict, ...]: + return tuple( + dict(zip( + [id_key, vals[0]], + (thread_op(item, replace_sex_code, replace_cross_info) + for item in items))) + for items in zip(ids, vals[1:])) + return (non_transposed, transposed) + def __default_process_value_transposed__( id_key: str, ids: tuple[str, ...], diff --git a/tests/r_qtl/test_files/test_covar.zip b/tests/r_qtl/test_files/test_covar.zip Binary files differindex 6fbb5e9..61961a0 100644 --- a/tests/r_qtl/test_files/test_covar.zip +++ b/tests/r_qtl/test_files/test_covar.zip diff --git a/tests/r_qtl/test_files/test_covar_transposed.zip b/tests/r_qtl/test_files/test_covar_transposed.zip Binary files differindex 5e933cc..c0758a3 100644 --- a/tests/r_qtl/test_files/test_covar_transposed.zip +++ b/tests/r_qtl/test_files/test_covar_transposed.zip diff --git a/tests/r_qtl/test_r_qtl2_covar.py b/tests/r_qtl/test_r_qtl2_covar.py index c18ee74..eef7a33 100644 --- a/tests/r_qtl/test_r_qtl2_covar.py +++ b/tests/r_qtl/test_r_qtl2_covar.py @@ -10,19 +10,21 @@ from r_qtl import r_qtl2 as rqtl2 @pytest.mark.parametrize( "filepath,expected", (("tests/r_qtl/test_files/test_covar.zip", - ({"id": "1", "sex": "m", "cross_direction": "(BxS)x(BxS)"}, - {"id": "2", "sex": "m", "cross_direction": "(BxS)x(BxS)"}, - {"id": "3", "sex": "m", "cross_direction": "(BxS)x(BxS)"}, - {"id": "146", "sex": "f", "cross_direction": "(BxS)x(BxS)"}, - {"id": "147", "sex": "f", "cross_direction": "(BxS)x(BxS)"}, - {"id": "148", "sex": "f", "cross_direction": "(BxS)x(BxS)"})), + ({"id": "1", "sex": "male", "cross_direction": 1}, + {"id": "2", "sex": "male", "cross_direction": 1}, + {"id": "3", "sex": "male", "cross_direction": 1}, + {"id": "71", "sex": "male", "cross_direction": 0}, + {"id": "72", "sex": "male", "cross_direction": 0}, + {"id": "146", "sex": "female", "cross_direction": 1}, + {"id": "147", "sex": "female", "cross_direction": 1}, + {"id": "148", "sex": "female", "cross_direction": 1})), ("tests/r_qtl/test_files/test_covar_transposed.zip", - ({"id": "1", "sex": "m", "cross_direction": "(BxS)x(BxS)"}, - {"id": "2", "sex": "m", "cross_direction": "(BxS)x(BxS)"}, - {"id": "3", "sex": "m", "cross_direction": "(BxS)x(BxS)"}, - {"id": "146", "sex": "f", "cross_direction": "(BxS)x(BxS)"}, - {"id": "147", "sex": "f", "cross_direction": "(BxS)x(BxS)"}, - {"id": "148", "sex": "f", "cross_direction": "(BxS)x(BxS)"})), + ({"id": "1", "sex": "male", "cross_direction": 1}, + {"id": "2", "sex": "male", "cross_direction": 1}, + {"id": "3", "sex": "male", "cross_direction": 1}, + {"id": "146", "sex": "female", "cross_direction": 1}, + {"id": "147", "sex": "female", "cross_direction": 1}, + {"id": "148", "sex": "female", "cross_direction": 1})), )) def test_parse_covar_files(filepath, expected): """Test parsing of 'covar' files from the R/qtl2 bundle. @@ -33,4 +35,6 @@ def test_parse_covar_files(filepath, expected): """ with ZipFile(Path(filepath).absolute(), "r") as zfile: cdata = rqtl2.control_data(zfile) - assert tuple(rqtl2.file_data(zfile, "covar", cdata)) == expected + process_fns = rqtl2.make_process_data_covar(cdata) + assert tuple( + rqtl2.file_data(zfile, "covar", cdata, *process_fns)) == expected |