def test_case_1(self):
query = OverallAssociationScoreQuery(ProgramSettings(target='ENSG00000157764'))
query.run()
self.assertAlmostEqual(query.min, 0.004)
self.assertAlmostEqual(query.max, 1.0)
self.assertAlmostEqual(query.average, 0.3404525)
self.assertAlmostEqual(query.standard_deviation, 0.339608)
def test_case_2(self):
query = OverallAssociationScoreQuery(ProgramSettings(disease='EFO_0002422'))
query.run()
self.assertAlmostEqual(query.min, 0.00000202)
self.assertAlmostEqual(query.max, 1.0)
self.assertAlmostEqual(query.average, 0.1253773)
self.assertAlmostEqual(query.standard_deviation, 0.1975769)
def test_case_3(self):
query = OverallAssociationScoreQuery(ProgramSettings(disease='EFO_0000616'))
query.run()
self.assertAlmostEqual(query.min, 0.000008090)
self.assertAlmostEqual(query.max, 1.0)
self.assertAlmostEqual(query.average, 0.4099038)
self.assertAlmostEqual(query.standard_deviation, 0.3367560)
self.assertAlmostEqual(query.standard_deviation, 0.339608)
def test_case_2(self):
query = OverallAssociationScoreQuery(ProgramSettings(disease='EFO_0002422'))
query.run()
self.assertAlmostEqual(query.min, 0.00000202)
self.assertAlmostEqual(query.max, 1.0)
self.assertAlmostEqual(query.average, 0.1253773)
self.assertAlmostEqual(query.standard_deviation, 0.1975769)
def test_case_3(self):
query = OverallAssociationScoreQuery(ProgramSettings(disease='EFO_0000616'))
query.run()
self.assertAlmostEqual(query.min, 0.000008090)
self.assertAlmostEqual(query.max, 1.0)
self.assertAlmostEqual(query.average, 0.4099038)
self.assertAlmostEqual(query.standard_deviation, 0.3367560)
if __name__ == '__main__':
settings = ProgramSettings.fromArgs(sys.argv[1:])
if settings.runTests:
unittest.main(defaultTest=['IntegrationTests'], argv=sys.argv[1:])
if settings.target == None and settings.disease == None:
print ("You must specify either a target (with -t) or a disease (with -d).")
exit(1)
query = OverallAssociationScoreQuery(settings)
query.run()
print(f'samples: {len(query.values)}; min: {query.min}; max: {query.max}; average: {query.average}; stddev: {query.standard_deviation}')
def test_default_settings(self):
settings = ProgramSettings.fromArgs([])
self.assertIsNone(settings.target)
self.assertIsNone(settings.disease)
self.assertFalse(settings.runTests)
def test_parse_runtests_arg(self):
settings = ProgramSettings.fromArgs(['--test'])
self.assertTrue(settings.runTests)
def test_parse_disease_arg(self):
settings = ProgramSettings.fromArgs(['-d', 'abc123'])
self.assertEqual(settings.disease, 'abc123')
def test_parse_target_arg(self):
settings = ProgramSettings.fromArgs(['-t', 'abc123'])
self.assertEqual(settings.target, 'abc123')