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"""Test cases for procedures defined in computations.rqtl"""
import unittest
from unittest import mock
import pytest
from gn3.computations.rqtl import generate_rqtl_cmd
class TestRqtl(unittest.TestCase):
"""Test cases for computations.rqtl module"""
@pytest.mark.unit_test
@mock.patch("gn3.computations.rqtl.generate_hash_of_string")
@mock.patch("gn3.computations.rqtl.get_hash_of_files")
def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
"""Test computing mapping results with R/qtl"""
mock_get_hash_files.return_value = "my-hash1"
mock_generate_hash_string.return_value = "my-hash2"
self.assertEqual(
generate_rqtl_cmd(rqtl_wrapper_cmd="scripts/rqtl_wrapper.R",
rqtl_wrapper_kwargs={
"g": "genofile",
"p": "phenofile",
"model": "normal",
"method": "hk",
"nperm": 1000,
"scale": "Mb",
"control": "rs123456"
},
rqtl_wrapper_bool_kwargs=[
"addcovar",
"interval"
]), {
"output_file":
"my-hash1my-hash2my-hash2-output.csv",
"rqtl_cmd": (
"Rscript scripts/rqtl_wrapper.R "
"--g genofile --p phenofile "
"--model normal --method hk "
"--nperm 1000 --scale Mb "
"--control rs123456 "
"--filename my-hash1my-hash2my-hash2-output.csv "
"--addcovar --interval"
)
})
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