diff options
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_run_mapping.py | 192 |
1 files changed, 167 insertions, 25 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index bba9de05..e925ad28 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -1,45 +1,187 @@ import unittest +import datetime from unittest import mock + from wqflask.marker_regression.run_mapping import get_genofile_samplelist from wqflask.marker_regression.run_mapping import geno_db_exists from wqflask.marker_regression.run_mapping import write_input_for_browser +from wqflask.marker_regression.run_mapping import export_mapping_results +from wqflask.marker_regression.run_mapping import trim_markers_for_figure + class AttributeSetter: - def __init__(self,obj): - for k,v in obj.items(): - setattr(self,k,v) + def __init__(self, obj): + for k, v in obj.items(): + setattr(self, k, v) class MockDataSetGroup(AttributeSetter): - - def get_genofiles(self): - return [{"location":"~/genofiles/g1_file","sample_list":["S1","S2","S3","S4"]}] + + def get_genofiles(self): + return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}] + + class TestRunMapping(unittest.TestCase): - def setUp(self): - self.group=MockDataSetGroup({"genofile":"~/genofiles/g1_file","name":"GP1_"}) - self.dataset=AttributeSetter({"group":self.group}) + 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}) + + def tearDown(self): + self.dataset = AttributeSetter( + {"group": {"location": "~/genofiles/g1_file"}}) + + def test_get_genofile_samplelist(self): + + results_1 = get_genofile_samplelist(self.dataset) + self.assertEqual(results_1, ["S1", "S2", "S3", "S4"]) + self.group.genofile = "~/genofiles/g2_file" + result_2 = get_genofile_samplelist(self.dataset) + self.assertEqual(result_2, []) + + @mock.patch("wqflask.marker_regression.run_mapping.data_set") + def test_geno_db_exists(self, mock_data_set): + mock_data_set.create_dataset.side_effect = [ + AttributeSetter({}), Exception()] + results_no_error = geno_db_exists(self.dataset) + results_with_error = geno_db_exists(self.dataset) + + self.assertEqual(mock_data_set.create_dataset.call_count, 2) + self.assertEqual(results_with_error, "False") + self.assertEqual(results_no_error, "True") + + + def test_trim_markers_for_figure(self): - def tearDown(self): - self.dataset=AttributeSetter({"group":{"location":"~/genofiles/g1_file"}}) - def test_get_genofile_samplelist(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 + }] - results_1=get_genofile_samplelist(self.dataset) - self.assertEqual(results_1,["S1","S2","S3","S4"]) - self.group.genofile="~/genofiles/g2_file" - result_2=get_genofile_samplelist(self.dataset) - self.assertEqual(result_2,[]) + 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 + } - @mock.patch("wqflask.marker_regression.run_mapping.data_set") - def test_geno_db_exists(self,mock_data_set): - mock_data_set.create_dataset.side_effect=[AttributeSetter({}),Exception()] - results_no_error=geno_db_exists(self.dataset) - results_with_error=geno_db_exists(self.dataset) + ] + self.assertEqual(results,expected) + self.assertEqual(result_2,marker_2) - self.assertEqual(mock_data_set.create_dataset.call_count,2) - self.assertEqual(results_with_error,"False") - self.assertEqual(results_no_error,"True") + 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)
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