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"""Test cases for procedures defined in computations.gemma"""
import unittest
from unittest import mock
from gn3.computations.gemma import generate_gemma_cmd
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"))
@mock.patch("gn3.computations.gemma.get_hash_of_files")
def test_compute_k_values_without_loco(self, mock_get_hash):
"""Test computing k valuse without loco"""
mock_get_hash.return_value = "my-hash"
self.assertEqual(
generate_gemma_cmd(gemma_cmd="gemma-wrapper",
output_dir="/tmp",
token="my-token",
gemma_kwargs={
"g": "genofile",
"p": "phenofile",
"a": "snpsfile"
}), {
"output_file":
"my-hash-output.json",
"gemma_cmd":
("gemma-wrapper --json -- -g genofile "
"-p phenofile -a snpsfile "
"-gk > /tmp/my-token/my-hash-output.json")
})
@mock.patch("gn3.computations.gemma.get_hash_of_files")
def test_generate_gemma_cmd_with_loco(self, mock_get_hash):
"""Test computing k valuse with loco"""
mock_get_hash.return_value = "my-hash"
self.assertEqual(
generate_gemma_cmd(gemma_cmd="gemma-wrapper",
output_dir="/tmp",
token="my-token",
chromosomes="1,2,3,4,5",
gemma_kwargs={
"g": "genofile",
"p": "phenofile",
"a": "snpsfile"
}), {
"output_file":
"my-hash-r+gF5a-output.json",
"gemma_cmd": ("gemma-wrapper --json "
"--loco --input 1,2,3,4,5 "
"-- -g genofile "
"-p phenofile -a snpsfile "
"-gk > /tmp/my-token/"
"my-hash-r+gF5a-output.json")
})
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