add tests for marker_regression/plink_mapping.py

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
--- /dev/null
+++ 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)