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"""Test the parsing of the R/qtl2 data 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(
"relpath,expected",
(("tests/r_qtl/test_files/test_gmap.zip",
({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
{"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
{"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
{"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
{"marker": "EC.66C", "chr": "1", "pos": "18.392830"})),
("tests/r_qtl/test_files/test_gmap_transposed.zip",
({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
{"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
{"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
{"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
{"marker": "EC.66C", "chr": "1", "pos": "18.392830"}))))
def test_parse_gmap_files(relpath, expected):
"""
GIVEN: A path to a zip file, `relpath`
WHEN: we parse a gmap file
THEN: ensure the parsed data is as expected.
"""
with ZipFile(Path(relpath).absolute(), "r") as zfile:
assert rqtl2.map_data(
zfile, "genetic-map", rqtl2.control_data(zfile)) == expected
@pytest.mark.skip(reason="Test not implemented yet.")
@pytest.mark.unit_test
@pytest.mark.parametrize(
"relpath,expected",
(("tests/r_qtl/test_files/test_pmap.zip",
()),
("tests/r_qtl/test_files/test_pmap_transposed.zip",
())))
def test_parse_pmap_files(relpath, expected):
"""
GIVEN: A path to a zip file, `relpath`
WHEN: we parse a pmap file
THEN: ensure the parsed data is as expected.
"""
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