Mercurial > repos > pieterlukasse > prims_metabolomics
annotate test/test_query_metexp_LARGE.py @ 47:646ca60a9ab0
removed tsv
author | pieter.lukasse@wur.nl |
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date | Sat, 15 Nov 2014 09:41:44 +0100 |
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1 '''Integration tests for the GCMS project''' |
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2 |
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3 from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611 |
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4 from GCMS import query_metexp |
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5 import os.path |
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6 import sys |
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7 import unittest |
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8 |
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9 |
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10 class IntegrationTest(unittest.TestCase): |
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11 |
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12 |
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13 # def test_MM_calculations(self): |
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14 # ''' |
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15 # test the implemented method for MM calculations for |
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16 # given chemical formulas |
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17 # ''' |
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18 # export_to_metexp_tabular.init_elements_and_masses_map() |
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19 # |
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20 # formula = "C8H18O3" |
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21 # # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26 |
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22 # result = export_to_metexp_tabular.get_molecular_mass(formula) |
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23 # self.assertEqual(162.26, result) |
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24 # |
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25 # formula = "CH2O3Fe2Ni" |
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26 # # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44 |
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27 # result = export_to_metexp_tabular.get_molecular_mass(formula) |
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28 # self.assertAlmostEqual(232.44, result, 2) |
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29 # |
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30 # |
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31 # |
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32 |
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33 |
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34 def test_large(self): |
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35 ''' |
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36 Simple test, but on larger set, last test executed in 28s |
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37 ''' |
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38 # Create out folder |
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39 outdir = "output/metexp_query/" |
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40 if not os.path.exists(outdir): |
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41 os.makedirs(outdir) |
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42 |
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43 #Build up arguments and run |
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44 |
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45 # input_file = sys.argv[1] |
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46 # molecular_mass_col = sys.argv[2] |
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47 # formula_col = sys.argv[3] |
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48 # metexp_dblink_file = sys.argv[4] |
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49 # output_result = sys.argv[5] |
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50 |
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51 input_file = resource_filename(__name__, "data/metexp_query_tabular_large.txt") |
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52 casid_col = "CAS" |
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53 formula_col = "FORMULA" |
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54 molecular_mass_col = "MM" |
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55 metexp_dblink_file = resource_filename(__name__, "data/METEXP Test DB.txt") |
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56 output_result = resource_filename(__name__, outdir + "metexp_query_results_added_LARGE.txt") |
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57 |
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58 sys.argv = ['test', |
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59 input_file, |
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60 casid_col, |
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61 formula_col, |
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62 molecular_mass_col, |
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63 metexp_dblink_file, |
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64 'GC', |
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65 output_result] |
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66 |
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67 # Execute main function with arguments provided through sys.argv |
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68 query_metexp.main() |
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69 |
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70 |
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71 |
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72 |
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73 def _read_file(filename): |
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74 ''' |
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75 Helper method to quickly read a file |
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76 @param filename: |
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77 ''' |
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78 with open(filename) as handle: |
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79 return handle.read() |