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-rw-r--r--wqflask/tests/wqflask/marker_regression/test_run_mapping.py192
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) \ No newline at end of file