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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": None},
{"id": "5", "liver": None, "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": None},
{"id": "5", "liver": None, "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:
cdata = rqtl2.control_data(zfile)
assert tuple(rqtl2.file_data(zfile, "pheno", cdata)) == expected
@pytest.mark.unit_test
@pytest.mark.parametrize(
"filepath,expected",
(("tests/r_qtl/test_files/test_phenocovar.zip",
({"id": "T0", "time (hrs)": "0"},
{"id": "T2", "time (hrs)": "0.0333333333333333"},
{"id": "T4", "time (hrs)": "0.0666666666666667"},
{"id": "T6", "time (hrs)": "0.1"},
{"id": "T8", "time (hrs)": "0.133333333333333"})),
("tests/r_qtl/test_files/test_phenocovar_transposed.zip",
({"id": "T0", "time (hrs)": "0"},
{"id": "T2", "time (hrs)": "0.0333333333333333"},
{"id": "T4", "time (hrs)": "0.0666666666666667"},
{"id": "T6", "time (hrs)": "0.1"},
{"id": "T8", "time (hrs)": "0.133333333333333"}))))
def test_parse_phenocovar_files(filepath, expected):
"""Test parsing of 'phenocovar' files from the R/qtl2 bundle.
GIVEN: path to a R/qtl2 bundle
WHEN: the 'phenocovar' file is parsed
THEN: verify the parsed data is as expected
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
cdata = rqtl2.control_data(zfile)
assert tuple(rqtl2.file_data(zfile, "phenocovar", cdata)) == expected
@pytest.mark.unit_test
@pytest.mark.parametrize(
"filepath,member,transposed,expected",
(("tests/r_qtl/test_files/test_pheno.zip",
"test_pheno.csv",
False,
("1", "2", "3", "4", "5")),
("tests/r_qtl/test_files/test_pheno_transposed.zip",
"test_pheno_transposed.csv",
True,
("1", "2", "3", "4", "5"))))
def test_load_geno_samples(filepath, member, transposed, expected):
assert sorted(rqtl2.load_samples(
filepath, member, transposed)) == sorted(expected)
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