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"""Test parsing of 'covar' 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(
"filepath,expected",
(("tests/r_qtl/test_files/test_covar.zip",
({"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": "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.
GIVEN: path to a R/qtl2 bundle
WHEN: the 'covar' file is parsed
THEN: verify the parsed data is as expected
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
cdata = rqtl2.control_data(zfile)
process_fns = rqtl2.make_process_data_covar(cdata)
assert tuple(
rqtl2.file_data(zfile, "covar", cdata, *process_fns)) == expected
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