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-rw-r--r--wqflask/tests/wqflask/marker_regression/test_run_mapping.py277
1 files changed, 144 insertions, 133 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
index e925ad28..6521c41d 100644
--- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
@@ -24,9 +24,11 @@ class MockDataSetGroup(AttributeSetter):
class TestRunMapping(unittest.TestCase):
def setUp(self):
self.group = MockDataSetGroup(
- {"genofile": "~/genofiles/g1_file", "name": "GP1_","species":"Human"})
- self.dataset = AttributeSetter({"fullname":"dataser_1","group": self.group,"type":"ProbeSet"})
- self.trait=AttributeSetter({"symbol":"IGFI","chr":"X1","mb":123313})
+ {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"})
+ self.dataset = AttributeSetter(
+ {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+ self.trait = AttributeSetter(
+ {"symbol": "IGFI", "chr": "X1", "mb": 123313})
def tearDown(self):
self.dataset = AttributeSetter(
@@ -51,137 +53,146 @@ class TestRunMapping(unittest.TestCase):
self.assertEqual(results_with_error, "False")
self.assertEqual(results_no_error, "True")
-
def test_trim_markers_for_figure(self):
-
- markers=[{
- "name":"MK1",
- "chr":"C1",
- "cM":"1",
- "Mb":"12000",
- "genotypes":[],
- "dominance":"TT",
- "additive":"VA",
- "lod_score":0.5
- },
- {
- "name":"MK2",
- "chr":"C2",
- "cM":"15",
- "Mb":"10000",
- "genotypes":[],
- "lod_score":0.7
- },
- {
- "name":"MK1",
- "chr":"C3",
- "cM":"45",
- "Mb":"1",
- "genotypes":[],
- "dominance":"Tt",
- "additive":"VE",
- "lod_score":1
- }]
-
- marker_2=[{
- "name":"MK1",
- "chr":"C1",
- "cM":"1",
- "Mb":"12000",
- "genotypes":[],
- "dominance":"TT",
- "additive":"VA",
- "p_wald":4.6
- }]
- results=trim_markers_for_figure(markers)
- result_2=trim_markers_for_figure(marker_2)
- expected=[
- {
- "name":"MK1",
- "chr":"C1",
- "cM":"1",
- "Mb":"12000",
- "genotypes":[],
- "dominance":"TT",
- "additive":"VA",
- "lod_score":0.5
- },
- {
- "name":"MK1",
- "chr":"C3",
- "cM":"45",
- "Mb":"1",
- "genotypes":[],
- "dominance":"Tt",
- "additive":"VE",
- "lod_score":1
- }
-
- ]
- self.assertEqual(results,expected)
- self.assertEqual(result_2,marker_2)
+ markers = [{
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "lod_score":0.5
+ },
+ {
+ "name": "MK2",
+ "chr": "C2",
+ "cM": "15",
+ "Mb": "10000",
+ "genotypes": [],
+ "lod_score":0.7
+ },
+ {
+ "name": "MK1",
+ "chr": "C3",
+ "cM": "45",
+ "Mb": "1",
+ "genotypes": [],
+ "dominance":"Tt",
+ "additive":"VE",
+ "lod_score":1
+ }]
+
+ marker_2 = [{
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "p_wald":4.6
+ }]
+ results = trim_markers_for_figure(markers)
+ result_2 = trim_markers_for_figure(marker_2)
+ expected = [
+ {
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "lod_score":0.5
+ },
+ {
+ "name": "MK1",
+ "chr": "C3",
+ "cM": "45",
+ "Mb": "1",
+ "genotypes": [],
+ "dominance":"Tt",
+ "additive":"VE",
+ "lod_score":1
+ }
+
+ ]
+ self.assertEqual(results, expected)
+ self.assertEqual(result_2, marker_2)
def test_export_mapping_results(self):
- datetime_mock=mock.Mock(wraps=datetime.datetime)
- datetime_mock.now.return_value=datetime.datetime(2019,9,1,10,12,12)
-
- markers=[{
- "name":"MK1",
- "chr":"C1",
- "cM":"1",
- "Mb":"12000",
- "genotypes":[],
- "dominance":"TT",
- "additive":"VA",
- "lod_score":3
- },
- {
- "name":"MK2",
- "chr":"C2",
- "cM":"15",
- "Mb":"10000",
- "genotypes":[],
- "lod_score":7
- },
- {
- "name":"MK1",
- "chr":"C3",
- "cM":"45",
- "Mb":"1",
- "genotypes":[],
- "dominance":"Tt",
- "additive":"VE",
- "lod_score":7
- }]
-
- with mock.patch("builtins.open", mock.mock_open()) as mock_open:
-
- # mock_open.assert_called_once_with("~/results","w+")
- # filehandler=mock_open()
- with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime",new=datetime_mock):
- export_mapping_results(dataset=self.dataset,trait=self.trait,markers=markers,results_path="~/results",mapping_scale="physic",score_type="-log(p)")
-
-
- write_calls=[
- mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
- mock.call('Population: Human GP1_\n'),mock.call('Data Set: dataser_1\n'),
- mock.call('Gene Symbol: IGFI\n'), mock.call('Location: X1 @ 123313 Mb\n'),
- mock.call('\n'), mock.call('Name,Chr,'),
- mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
- mock.call(',Additive'),mock.call(',Dominance'),
- mock.call('\n'),mock.call('MK1,C1,'),
- mock.call('12000,'), mock.call('1,'),
- mock.call('3'), mock.call(',VA'),
- mock.call(',TT'),mock.call('\n'),
- mock.call('MK2,C2,'),mock.call('10000,'),
- mock.call('15,'), mock.call('7'),
- mock.call('\n'), mock.call('MK1,C3,'),
- mock.call('1,'),mock.call('45,'),
- mock.call('7'), mock.call(',VE'),
- mock.call(',Tt')
-
- ]
- mock_open.assert_called_once_with("~/results","w+")
- filehandler=mock_open()
- filehandler.write.assert_has_calls(write_calls) \ No newline at end of file
+ datetime_mock = mock.Mock(wraps=datetime.datetime)
+ datetime_mock.now.return_value = datetime.datetime(
+ 2019, 9, 1, 10, 12, 12)
+
+ markers = [{
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "lod_score":3
+ },
+ {
+ "name": "MK2",
+ "chr": "C2",
+ "cM": "15",
+ "Mb": "10000",
+ "genotypes": [],
+ "lod_score":7
+ },
+ {
+ "name": "MK1",
+ "chr": "C3",
+ "cM": "45",
+ "Mb": "1",
+ "genotypes": [],
+ "dominance":"Tt",
+ "additive":"VE",
+ "lod_score":7
+ }]
+
+ with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+
+ with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
+ export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
+ results_path="~/results", mapping_scale="physic", score_type="-log(p)")
+
+ write_calls = [
+ mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
+ mock.call('Population: Human GP1_\n'), mock.call(
+ 'Data Set: dataser_1\n'),
+ mock.call('Gene Symbol: IGFI\n'), mock.call(
+ 'Location: X1 @ 123313 Mb\n'),
+ mock.call('\n'), mock.call('Name,Chr,'),
+ mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
+ mock.call(',Additive'), mock.call(',Dominance'),
+ mock.call('\n'), mock.call('MK1,C1,'),
+ mock.call('12000,'), mock.call('1,'),
+ mock.call('3'), mock.call(',VA'),
+ mock.call(',TT'), mock.call('\n'),
+ mock.call('MK2,C2,'), mock.call('10000,'),
+ mock.call('15,'), mock.call('7'),
+ mock.call('\n'), mock.call('MK1,C3,'),
+ mock.call('1,'), mock.call('45,'),
+ mock.call('7'), mock.call(',VE'),
+ mock.call(',Tt')
+
+ ]
+ mock_open.assert_called_once_with("~/results", "w+")
+ filehandler = mock_open()
+ filehandler.write.assert_has_calls(write_calls)
+
+
+ @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+ def test_write_input_for_browser(self,mock_choice):
+ mock_choice.side_effect=["F","i","l","e","s","x"]
+ with mock.patch("builtins.open",mock.mock_open()) as mock_open:
+ expected=['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT']
+
+ results=write_input_for_browser(this_dataset=self.dataset,gwas_results={},annotations={})
+ self.assertEqual(results,expected)
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-03 14:54:39 +0000