diff options
| -rw-r--r-- | r_qtl/r_qtl2.py | 35 | ||||
| -rw-r--r-- | tests/r_qtl/test_files/test_cross_info_01.zip | bin | 597 -> 594 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_files/test_cross_info_02.zip | bin | 778 -> 775 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_files/test_sex_info_01.zip | bin | 0 -> 589 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_files/test_sex_info_02.zip | bin | 0 -> 773 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_sex_information.py | 35 |
6 files changed, 63 insertions, 7 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 02217ee..2c1e162 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -134,6 +134,13 @@ def make_process_data_geno(cdata) -> tuple[ for items in zip(ids, vals[1:])) return (__non_transposed__, __transposed__) +def replace_sex_info(val, cdata: dict): + """Replace sex information in files with values in the control data.""" + sex_info = cdata.get("sex", False) + if bool(sex_info): + return sex_info.get(val, val) + return val + def replace_cross_info(val, cdata: dict): """ Replace cross information in files with the values in the control data. @@ -148,15 +155,11 @@ def make_process_data_covar(cdata) -> tuple[ 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 + rep_sex_info = partial(replace_sex_info, cdata=cdata) rep_cross_info = partial(replace_cross_info, cdata=cdata) def non_transposed(row: dict) -> dict: return { - key: thread_op(value, replace_sex_code, rep_cross_info) + key: thread_op(value, rep_sex_info, rep_cross_info) for key,value in row.items() } def transposed(id_key: str, @@ -165,7 +168,7 @@ def make_process_data_covar(cdata) -> tuple[ return tuple( dict(zip( [id_key, vals[0]], - (thread_op(item, replace_sex_code, rep_cross_info) + (thread_op(item, rep_sex_info, rep_cross_info) for item in items))) for items in zip(ids, vals[1:])) return (non_transposed, transposed) @@ -221,3 +224,21 @@ def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: yield { key: thread_op(value, partial(replace_cross_info, cdata=cdata)) for key, value in row.items() if key not in sex_fields} + +def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: + """Load cross information where present.""" + cdata_sex_info = cdata.get("sex", {}) + sex_info_file_key = "covar" + new_cdata = {**cdata} + ci_fields = (cdata.get("cross_info",{}).get("covar",""),) + if "file" in cdata_sex_info: + sex_info_file_key = "gnqc_sex_info_file" + new_cdata = {**cdata, "gnqc_sex_info_file": cdata_sex_info["file"]} + + for row in file_data(zfile, + sex_info_file_key, + new_cdata, + *make_process_data_covar(cdata)): + yield { + key: thread_op(value, partial(replace_sex_info, cdata=cdata)) + for key, value in row.items() if key not in ci_fields} diff --git a/tests/r_qtl/test_files/test_cross_info_01.zip b/tests/r_qtl/test_files/test_cross_info_01.zip index 1211f96..6143a9f 100644 --- a/tests/r_qtl/test_files/test_cross_info_01.zip +++ b/tests/r_qtl/test_files/test_cross_info_01.zip Binary files differdiff --git a/tests/r_qtl/test_files/test_cross_info_02.zip b/tests/r_qtl/test_files/test_cross_info_02.zip index dddd281..7e23fc4 100644 --- a/tests/r_qtl/test_files/test_cross_info_02.zip +++ b/tests/r_qtl/test_files/test_cross_info_02.zip Binary files differdiff --git a/tests/r_qtl/test_files/test_sex_info_01.zip b/tests/r_qtl/test_files/test_sex_info_01.zip new file mode 100644 index 0000000..bc60d84 --- /dev/null +++ b/tests/r_qtl/test_files/test_sex_info_01.zip Binary files differdiff --git a/tests/r_qtl/test_files/test_sex_info_02.zip b/tests/r_qtl/test_files/test_sex_info_02.zip new file mode 100644 index 0000000..c862b73 --- /dev/null +++ b/tests/r_qtl/test_files/test_sex_info_02.zip Binary files differdiff --git a/tests/r_qtl/test_r_qtl2_sex_information.py b/tests/r_qtl/test_r_qtl2_sex_information.py new file mode 100644 index 0000000..90eae8d --- /dev/null +++ b/tests/r_qtl/test_r_qtl2_sex_information.py @@ -0,0 +1,35 @@ +"""Test loading of sex information.""" + +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( + "filepath,expected", + (("tests/r_qtl/test_files/test_sex_info_01.zip", + ({"id": "1", "sex": "male"}, + {"id": "2", "sex": "male"}, + {"id": "3", "sex": "male"}, + {"id": "71", "sex": "male"}, + {"id": "72", "sex": "male"}, + {"id": "146", "sex": "female"}, + {"id": "147", "sex": "female"}, + {"id": "148", "sex": "female"})), + ("tests/r_qtl/test_files/test_sex_info_02.zip", + ({"id": "1", "sex": "male"}, + {"id": "2", "sex": "male"}, + {"id": "3", "sex": "male"}, + {"id": "71", "sex": "male"}, + {"id": "72", "sex": "male"}, + {"id": "146", "sex": "female"}, + {"id": "147", "sex": "female"}, + {"id": "148", "sex": "female"})))) +def test_parse_sex_info(filepath, expected): + """Test parsing of sex information.""" + with ZipFile(Path(filepath).absolute(), "r") as zfile: + assert tuple(rqtl2.sex_information( + zfile, rqtl2.control_data(zfile))) == expected |