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"""Test cases for procedures defined in computations.gemma"""
import unittest
from unittest import mock
from gn3.computations.gemma import generate_pheno_txt_file
class TestGemma(unittest.TestCase):
"""Test cases for computations.gemma module"""
def test_generate_pheno_txt_file(self):
"""Test that the pheno text file is generated correctly"""
open_mock = mock.mock_open()
with mock.patch("gn3.computations.gemma.open",
open_mock, create=True):
_file = generate_pheno_txt_file(tmpdir="/tmp",
trait_filename="phenotype.txt",
values=["x", "x", "BXD07 438.700"])
self.assertEqual(_file, "/tmp/gn2/phenotype.txt")
open_mock.assert_called_with("/tmp/gn2/phenotype.txt", "w")
open_mock.return_value.write.assert_has_calls([
mock.call("NA\n"),
mock.call("NA\n"),
mock.call("BXD07 438.700\n")])
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