diff options
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_run_mapping.py | 277 |
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) |