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comparison test/test_export_to_metexp_tabular.py @ 21:19d8fd10248e

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* Added interface to METEXP data store, including tool to fire queries in batch mode * Improved quantification output files of MsClust, a.o. sorting mass list based on intensity (last two columns of quantification files) * Added Molecular Mass calculation method
author pieter.lukasse@wur.nl
date Wed, 05 Mar 2014 17:20:11 +0100
parents 9d5f4f5f764b
children
comparison
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20:24fb75fedee0 21:19d8fd10248e
7 import unittest 7 import unittest
8 8
9 9
10 class IntegrationTest(unittest.TestCase): 10 class IntegrationTest(unittest.TestCase):
11 11
12
13 def test_MM_calculations(self):
14 '''
15 test the implemented method for MM calculations for
16 given chemical formulas
17 '''
18 export_to_metexp_tabular.init_elements_and_masses_map()
19
20 formula = "C8H18O3"
21 # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26
22 result = export_to_metexp_tabular.get_molecular_mass(formula)
23 self.assertEqual(162.26, result)
24
25 formula = "CH2O3Fe2Ni"
26 # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44
27 result = export_to_metexp_tabular.get_molecular_mass(formula)
28 self.assertAlmostEqual(232.44, result, 2)
29
30
31
32
12 33
13 def test_combine_output_simple(self): 34 def test_combine_output_simple(self):
14 ''' 35 '''
15 comment me 36 comment me
16 ''' 37 '''
26 output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt") 47 output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt")
27 48
28 sys.argv = ['test', 49 sys.argv = ['test',
29 rankfilter_and_caslookup_combined_file, 50 rankfilter_and_caslookup_combined_file,
30 msclust_quantification_and_spectra_file, 51 msclust_quantification_and_spectra_file,
31 output_csv] 52 output_csv,
53 'tomato',
54 'leafs',
55 'test experiment',
56 'pieter',
57 'DB5 column']
58
32 # Execute main function with arguments provided through sys.argv 59 # Execute main function with arguments provided through sys.argv
33 export_to_metexp_tabular.main() 60 export_to_metexp_tabular.main()
34 61
35 ''' 62 '''
36 # Asserts are based on reading in with process_data and comparing values of 63 # Asserts are based on reading in with process_data and comparing values of