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-rw-r--r--wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py43
1 files changed, 9 insertions, 34 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py
index fd45fd65..963c131f 100644
--- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py
@@ -21,13 +21,6 @@ class MockDatasetGroup(AttributeSetter):
class TestGemmaMapping(unittest.TestCase):
- # def test_fail(self):
- # self.assertEqual(2,3)
-
- def setUp(self):
- pass
-
-
@mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco):
@@ -36,7 +29,6 @@ class TestGemmaMapping(unittest.TestCase):
output_files = "file1"
use_loco = False
- mock_parse_loco.side_effect = None
mock_parse_loco.return_value = []
this_trait = AttributeSetter({"name": "t1"})
@@ -46,7 +38,6 @@ class TestGemmaMapping(unittest.TestCase):
expected_results = ([], "file1")
self.assertEqual(expected_results, result)
-
@mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
@mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
@mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
@@ -59,7 +50,7 @@ class TestGemmaMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R")
@mock.patch("wqflask.marker_regression.gemma_mapping.os")
@mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
- def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files,mock_logger,mock_parse_loco):
+ def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco):
chromosomes = []
for i in range(1, 5):
@@ -75,35 +66,28 @@ class TestGemmaMapping(unittest.TestCase):
trait = AttributeSetter({"name": "trait1"})
samples = []
- mock_gen_pheno_txt.side_effect = None
+
mock_gen_pheno_txt.return_value = None
mock_os.path.isfile.return_value = True
- mock_os.system.return_value = None
- mock_os.system.side_effect = None
- mock_gen_covar.side_effect = None
mock_gen_covar.return_value = None
mock_flat_files.return_value = "/home/genotype/bimbam"
- mock_parse_loco.side_effect = None
mock_parse_loco.return_value = []
results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
], vals=[], covariates="", use_loco=True)
- # check results
self.assertEqual(results, ([], "GP1_GWA_RRRRRR"))
mock_gen_pheno_txt.assert_called_once()
self.assertEqual(mock_flat_files.call_count, 4)
-
-
system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'),
mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')]
mock_os.system.assert_has_calls(system_calls)
- mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt'))
+ mock_os.path.isfile.assert_called_once_with(
+ ('/home/user/imgfile_output.assoc.txt'))
- self.assertEqual(mock_logger.debug.call_count,2)
-
+ self.assertEqual(mock_logger.debug.call_count, 2)
- mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR")
+ mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR")
@mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data")
def test_gen_pheno_txt_file(self):
@@ -144,7 +128,6 @@ class TestGemmaMapping(unittest.TestCase):
with mock.patch("builtins.open", mock.mock_open())as mock_open:
gen_covariates_file(this_dataset=this_dataset, covariates=covariates,
samples=["x1", "x2", "X3"])
- # test mocked methods
create_dataset.assert_has_calls(
[mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')])
@@ -157,13 +140,10 @@ class TestGemmaMapping(unittest.TestCase):
create_trait.assert_has_calls(mock_calls)
- # test writing of covariates.txt
-
flat_files.assert_called_once_with('mapping')
mock_open.assert_called_once_with(
'Home/Genenetwork/group_X_covariates.txt', 'w')
filehandler = mock_open()
- # expected all-9
filehandler.write.assert_has_calls([mock.call(
'-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
@@ -186,23 +166,18 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4
self.assertEqual(results, expected)
@mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
- def test_xparse_gemma_output_empty_return(self):
+ def test_parse_gemma_output_empty_return(self):
output_file_results = """chr\t today"""
with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open:
results = parse_gemma_output(genofile_name="gema_file")
self.assertEqual(results, [])
- @mock.patch("builtins.open", mock.mock_open(read_data="chr\t"))
- def test_parse_gemma_output_empty_return(self):
- # duplicate
- string_read = parse_gemma_output(genofile_name="hdf")
- # print(string_read)
-
@mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
@mock.patch("wqflask.marker_regression.gemma_mapping.os")
def test_parse_loco_output_file_found(self, mock_os):
- mock_os.path.isfile.return_value = False
+ mock_os.path.isfile.return_value = True
file_to_write = """{"files":["file_1","file_2"]}"""
+ #incomplete
@mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
@mock.patch("wqflask.marker_regression.gemma_mapping.os")