Mercurial > repos > pieterlukasse > prims_metabolomics
diff rankfilter_GCMS/test/test_rankfilter.py @ 0:9d5f4f5f764b
Initial commit to toolshed
author | pieter.lukasse@wur.nl |
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date | Thu, 16 Jan 2014 13:10:00 +0100 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rankfilter_GCMS/test/test_rankfilter.py Thu Jan 16 13:10:00 2014 +0100 @@ -0,0 +1,58 @@ +''' +Created on Mar 13, 2012 + +@author: marcelk +''' +from GCMS.rankfilter_GCMS.rankfilter import get_data, calibrate, calibrate_poly, convert_rt, convert_rt_poly +from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611 +import unittest + + +class Test(unittest.TestCase): + + def setUp(self): + self.calibration = resource_filename(__name__, "data/calibration.txt") + self.sample = resource_filename(__name__, "data/sample.txt") + + def test_get_data(self): + samples = get_data(self.sample, ['CAS', 'Name', 'R.T.', 'Forward', 'Reverse', 'Formula']) + self.assertEqual(['C29H50O', 'C29H50O', 'C29H50O', 'C29H50O', 'C29H50O', 'C28H48O', 'C28H48O', 'C28H48O', + 'C28H48O', 'C27H44O2', 'C29H50O2', 'C29H50O2', 'C29H50O2', 'C29H50O2', 'C29H50O2', + 'C28H48O2', 'C28H48O2', 'C28H48O2', 'C28H48O2', 'C30H50O3', 'C29H50O', 'C29H50O', + 'C29H50O', 'C29H50O'], samples['Formula']) + + def test_calibrate(self): + standards = get_data(self.calibration, ['Name', 'R.T.', 'RI']) + coeff = calibrate(standards) + self.assertAlmostEqual(103.19073523551653, coeff[0], 5) + self.assertAlmostEqual(277.14374835349395, coeff[1], 5) + + def test_calibrate_poly(self): + standards = get_data(self.calibration, ['Name', 'R.T.', 'RI']) + poly_cal = calibrate_poly(standards) + self.assertAlmostEqual(0.028897105229818407, poly_cal[0], 5) + self.assertAlmostEqual(0.704572097468386, poly_cal[1], 5) + self.assertAlmostEqual(51.636852478526357, poly_cal[2], 5) + self.assertAlmostEqual(704.95499738104672, poly_cal[3], 5) + + def test_convert_rt(self): + standards = get_data(self.calibration, ['Name', 'R.T.', 'RI']) + coeff = calibrate(standards) + convert = convert_rt({'R.T.': [5, 10, 15, 20]}, coeff) + self.assertAlmostEqual(793.09742453, convert['RIexp'][0], 5) + self.assertAlmostEqual(1309.05110071, convert['RIexp'][1], 5) + self.assertAlmostEqual(1825.00477689, convert['RIexp'][2], 5) + self.assertAlmostEqual(2340.95845306, convert['RIexp'][3], 5) + + def test_convert_rt_poly(self): + standards = get_data(self.calibration, ['Name', 'R.T.', 'RI']) + poly_cal = calibrate_poly(standards) + convert = convert_rt_poly({'R.T.': [5, 10, 15, 20]}, poly_cal) + self.assertAlmostEqual(984.36570036, convert['RIexp'][0], 5) + self.assertAlmostEqual(1320.67783714, convert['RIexp'][1], 5) + self.assertAlmostEqual(1735.56423664, convert['RIexp'][2], 5) + self.assertAlmostEqual(2250.69772778, convert['RIexp'][3], 5) + +if __name__ == "__main__": + #import sys;sys.argv = ['', 'Test.testName'] + unittest.main()