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"""Test parsing of pheno files in a R/qtl2 bundle."""
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_pheno.zip",
({"id": "1", "liver": "61.92", "spleen": "153.16"},
{"id": "2", "liver": "88.33", "spleen": "178.58"},
{"id": "3", "liver": "58", "spleen": "131.91"},
{"id": "4", "liver": "78.06", "spleen": "126.13"},
{"id": "5", "liver": "65.31", "spleen": "181.05"})),
("tests/r_qtl/test_files/test_pheno_transposed.zip",
({"id": "1", "liver": "61.92", "spleen": "153.16"},
{"id": "2", "liver": "88.33", "spleen": "178.58"},
{"id": "3", "liver": "58", "spleen": "131.91"},
{"id": "4", "liver": "78.06", "spleen": "126.13"},
{"id": "5", "liver": "65.31", "spleen": "181.05"}))))
def test_parse_pheno_files(filepath, expected):
"""Test parsing of 'pheno' files from the R/qtl2 bundle.
GIVEN: path to a R/qtl2 bundle
WHEN: the 'pheno' file is parsed
THEN: verify the parsed data is as expected
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
assert tuple(
rqtl2.phenotype_data(zfile, rqtl2.control_data(zfile))) == expected
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