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"""Test the parsing of control file"""
from pathlib import Path
import pytest
from zipfile import ZipFile
from r_qtl import r_qtl2 as rqtl2
__DEFAULTS__ = {
"description": "Empty control file to test defaults",
"sep": ",",
"na.strings": ["NA"],
"comment.char": "#",
"geno_transposed": False,
"founder_geno_transposed": False,
"pheno_transposed": False,
"covar_transposed": False,
"phenocovar_transposed": False,
"gmap_transposed": False,
"pmap_transposed": False,
"phenose_transposed": False
}
@pytest.mark.unit_test
@pytest.mark.parametrize(
"filepath,expected",
(("tests/r_qtl/test_files/empty_control_file_yaml.zip",
__DEFAULTS__),
("tests/r_qtl/test_files/empty_control_file_json.zip",
__DEFAULTS__)))
def test_defaults_are_set(filepath, expected):
"""
GIVEN: path to a R/qtl2 bundle with an empty control file
WHEN: the control data is parsed
THEN: ensure all the defaults are set up correctly
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
assert rqtl2.control_data(zfile) == expected
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