comparison test/test_export_to_metexp_tabular.py @ 21:19d8fd10248e

* 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

20:24fb75fedee0

import unittest


class IntegrationTest(unittest.TestCase):


    def test_combine_output_simple(self):
        '''
        comment me
        '''

        output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt")
    
        sys.argv = ['test',
                    rankfilter_and_caslookup_combined_file,
                    msclust_quantification_and_spectra_file,
                    output_csv]
        # Execute main function with arguments provided through sys.argv
        export_to_metexp_tabular.main()

        '''
        # Asserts are based on reading in with process_data and comparing values of 

21:19d8fd10248e

import unittest


class IntegrationTest(unittest.TestCase):


    def test_MM_calculations(self):
        '''
        test the implemented method for MM calculations for 
        given chemical formulas
        '''
        export_to_metexp_tabular.init_elements_and_masses_map()
        
        formula = "C8H18O3"
        # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26
        result = export_to_metexp_tabular.get_molecular_mass(formula)
        self.assertEqual(162.26, result)
        
        formula = "CH2O3Fe2Ni"
        # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44
        result = export_to_metexp_tabular.get_molecular_mass(formula)
        self.assertAlmostEqual(232.44, result, 2)
        
        
        
        

    def test_combine_output_simple(self):
        '''
        comment me
        '''

        output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt")
    
        sys.argv = ['test',
                    rankfilter_and_caslookup_combined_file,
                    msclust_quantification_and_spectra_file,
                    output_csv, 
                    'tomato',
                    'leafs',
                    'test experiment',
                    'pieter',
                    'DB5 column']
        
        # Execute main function with arguments provided through sys.argv
        export_to_metexp_tabular.main()

        '''
        # Asserts are based on reading in with process_data and comparing values of