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authorAlexanderlacuna2020-11-08 22:04:52 +0300
committerAlexanderlacuna2020-11-08 22:04:52 +0300
commit5e50e19a014efdfcf0ce1397025879d4ada4d271 (patch)
tree253f309ff43d869345c5710aebbcadb1dc4e845f /wqflask/tests
parent8e55eaf473d98c1d165fcaf60ab0e24abb6acd9e (diff)
downloadgenenetwork2-5e50e19a014efdfcf0ce1397025879d4ada4d271.tar.gz
add tests for marker_regression/plink_mapping.py
Diffstat (limited to 'wqflask/tests')
-rw-r--r--wqflask/tests/wqflask/marker_regression/test_plink_mapping.py83
1 files changed, 83 insertions, 0 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py
new file mode 100644
index 00000000..b827fd0f
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+++ b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py
@@ -0,0 +1,83 @@
+# test for wqflask/marker_regression/plink_mapping.py
+import unittest
+from unittest import mock
+from wqflask.marker_regression.plink_mapping import build_line_list
+from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file
+from wqflask.marker_regression.plink_mapping import flat_files
+from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink
+from wqflask.marker_regression.plink_mapping import parse_plink_output
+
+
+class AttributeSetter:
+ def __init__(self, obj):
+ for key, val in obj.items():
+ setattr(self, key, val)
+
+
+class TestPlinkMapping(unittest.TestCase):
+
+ def test_build_line_list(self):
+ line_1 = "this is line one test"
+ irregular_line = " this is an, irregular line "
+ exp_line1 = ["this", "is", "line", "one", "test"]
+
+ results = build_line_list(irregular_line)
+ self.assertEqual(exp_line1, build_line_list(line_1))
+ self.assertEqual([], build_line_list())
+ self.assertEqual(["this", "is", "an,", "irregular", "line"], results)
+
+ @mock.patch("wqflask.marker_regression.plink_mapping.flat_files")
+ def test_get_samples_from_ped_file(self, mock_flat_files):
+ dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
+ file_sample = """Expected_1\tline test
+Expected_2\there
+ Expected_3\tthree"""
+ mock_flat_files.return_value = "/home/user/"
+ with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open:
+ results = get_samples_from_ped_file(dataset)
+ mock_flat_files.assert_called_once_with("mapping")
+ mock_open.assert_called_once_with("/home/user/n_1.ped", "r")
+ self.assertEqual(
+ ["Expected_1", "Expected_2", "Expected_3"], results)
+
+ @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+ @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file")
+ def test_gen_pheno_txt_file_plink(self, mock_samples):
+ mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"]
+
+ trait = AttributeSetter({"name": "TX"})
+ dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
+ vals = ["value=K1", "value=K2", "value=K3"]
+ with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+ results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset,
+ vals=vals, pheno_filename="ph_file")
+ mock_open.assert_called_once_with(
+ "/home/user/data/ph_file.txt", "wb")
+ filehandler = mock_open()
+ calls_expected = [mock.call('FID\tIID\tTX\n'),
+ mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')]
+
+ filehandler.write.assert_has_calls(calls_expected)
+
+ filehandler.close.assert_called_once()
+
+ @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+ @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list")
+ def test_parse_plink_output(self, mock_line_list):
+ chromosomes = [0, 34, 110, 89, 123, 23, 2]
+ species = AttributeSetter(
+ {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})})
+
+ fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA"""
+
+ mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [
+ "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]]
+ # print("sdfsfdf",species.chromosomes)
+ with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open:
+ parse_results = parse_plink_output(
+ output_filename="P1_file", species=species)
+ mock_open.assert_called_once_with(
+ "/home/user/data/P1_file.qassoc", "rb")
+ expected = (2, {'AACCAT': 0.89, 'AATA': 0.3})
+
+ self.assertEqual(parse_results, expected)