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"""Test cases for procedures defined in computations.gemma"""
import unittest
from unittest import mock
from gn3.computations.gemma import generate_hash_of_string
from gn3.computations.gemma import generate_pheno_txt_file
from gn3.computations.gemma import generate_gemma_computation_cmd
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_"
"P7y6QWnwBPedSZdL0+m/GQ.txt"))
open_mock.assert_called_with(("/tmp/gn2/phenotype_"
"P7y6QWnwBPedSZdL0+m/GQ.txt"), "w")
open_mock.return_value.write.assert_has_calls([
mock.call("NA\n"),
mock.call("NA\n"),
mock.call("BXD07 438.700\n")])
def test_generate_hash_of_string(self):
"""Test that a string is hashed correctly"""
self.assertEqual(generate_hash_of_string("I^iQP&TlSR^z"),
"hMVRw8kbEp49rOmoIkhMjA")
@mock.patch("gn3.computations.gemma.do_paths_exist")
def test_compose_k_computation_cmd(self, mock_pathsp):
"""Test that a K computation cmd is constructed properly"""
mock_pathsp.return_value = True
self.assertEqual(
generate_gemma_computation_cmd(
gemma_cmd="gemma-wrapper",
gemma_wrapper_kwargs=None,
gemma_kwargs={
"geno_filename": "genofile.txt",
"trait_filename": "test.txt",
"covar_filename": "genofile_snps.txt"},
output_file="/tmp/gn2/k_output_gUFhGu4rLG7k+CXLPk1OUg.txt",
),
("gemma-wrapper --json -- "
"-g genofile.txt -p "
"test.txt -a genofile_snps.txt "
"-gk > /tmp/gn2/"
"k_output_gUFhGu4rLG7k+CXLPk1OUg.txt"))
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