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1 '''
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2 Created on Mar 6, 2012
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3
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4 @author: marcelk
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5 '''
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6 from GCMS import library_lookup, match_library
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7 from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611
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8 import os
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9 import shutil
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10 import tempfile
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11 import unittest
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12
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13
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14 class Test(unittest.TestCase):
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15 '''
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16 Tests the 'library_lookup' Galaxy tool
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17 '''
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18
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19 def setUp(self):
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20 self.ri_database = resource_filename(__name__, "data/RIDB_subset.txt")
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21 self.nist_output = resource_filename(__name__, "data/NIST_tabular.txt")
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22 self.ridb_poly_regress = resource_filename(__name__, "data/ridb_poly_regression.txt")
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23 self.ridb_linear_regress = resource_filename(__name__, "data/ridb_linear_regression.txt")
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24
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25 def test_create_lookup_table(self):
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26 '''
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27 Tests the 'create_lookup_table' function
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28 '''
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29 column_type = 'Capillary'
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30 polarity = 'Semi-standard non-polar'
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31 lookup_dict = library_lookup.create_lookup_table(self.ri_database, column_type, polarity)
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32 self.assertFalse(False in [res[4] == 'Capillary' for res in lookup_dict['4177166']])
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33 self.assertEqual(['C51276336', '2,6-Dimethyl-octa-1,7-dien-3,6-diol', 'C10H18O2',
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34 '1277', 'Capillary', 'Semi-standard non-polar', 'DB-5MS', '1',
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35 'C51276336_DB-5MS', '', '', ''], lookup_dict['51276336'][1])
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36
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37 def test_read_model(self):
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38 '''
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39 Tests reading the regression model data containing the parameters required for converting
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40 retention indices between GC-columns
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41 '''
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42 model, _ = library_lookup._read_model(self.ridb_poly_regress)
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43 # Order of values: coefficient 1 through 4, left limit, right limit
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44 # Polynomial model
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45 self.assertEqual([20.6155874639486, 0.945187096379008, 3.96480787567566e-05, -9.04377237159287e-09,
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46 628.0, 2944.0, 405.0, 0, 0.998685262365514], model['HP-5']['SE-54'])
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47 self.assertEqual([-92.3963391356951, 1.26116176393346, -0.000191991657547972, 4.15387371263164e-08,
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48 494.0, 2198.0, 407.0, 0, 0.996665023122993], model['Apiezon L']['Squalane'])
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49 # Linear model
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50 model, _ = library_lookup._read_model(self.ridb_linear_regress)
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51 self.assertEqual([2.81208738561543, 0.99482475526584, 628.0, 2944.0, 405.0, 0, 0.998643883946458],
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52 model['HP-5']['SE-54'])
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53 self.assertEqual([19.979922768462, 0.993741869298272, 494.0, 2198.0, 407.0, 0, 0.99636062891041],
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54 model['Apiezon L']['Squalane'])
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55
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56 def test_apply_regression(self):
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57 '''
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58 Tests the regression model on some arbitrary retention indices
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59 '''
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60 poly_model, _ = library_lookup._read_model(self.ridb_poly_regress)
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61 linear_model, _ = library_lookup._read_model(self.ridb_linear_regress)
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62 retention_indices = [1000, 1010, 1020, 1030, 1040, 1050]
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63 converted_poly = []
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64 converted_linear = []
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65 for ri in retention_indices:
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66 converted_poly.append(library_lookup._apply_poly_regression('HP-5', 'DB-5', ri, poly_model))
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67 converted_linear.append(library_lookup._apply_linear_regression('HP-5', 'DB-5', ri, linear_model))
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68
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69 self.assertEqual([1003.0566541860778, 1013.0979459524663, 1023.1358645806529, 1033.170466241159,
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70 1043.2018071045052, 1053.2299433412131], converted_poly)
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71 self.assertEqual([1001.8127584915925, 1011.830140783027, 1021.8475230744615, 1031.864905365896,
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72 1041.8822876573306, 1051.899669948765], converted_linear)
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73
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74 # Test polynomial limit detection, the following RI falls outside of the possible limits
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75 ri = 3400
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76 converted_poly = library_lookup._apply_poly_regression('HP-5', 'DB-5', ri, poly_model)
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77 self.assertEqual(False, converted_poly)
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78
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79 def test_preferred_hit(self):
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80 ''' Tests the matching of the hits with the preferred column, including regression '''
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81 model, method = library_lookup._read_model(self.ridb_poly_regress)
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82 column_type = 'Capillary'
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83 polarity = 'Semi-standard non-polar'
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84 lookup_dict = library_lookup.create_lookup_table(self.ri_database, column_type, polarity)
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85 hits = lookup_dict['150867']
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86 # No regression, should however consider order of given preference
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87 match = library_lookup._preferred(hits, ['SE-52', 'DB-5', 'HP-5'], column_type, polarity, model, method)
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88 expected = (['C150867', '(E)-phytol', 'C20H40O', '2110', 'Capillary',
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89 'Semi-standard non-polar', 'SE-52', '', 'C150867_SE-52', '', '', ''], False)
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90 self.assertEqual(expected, match)
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91
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92 # Perform regression by looking for 'OV-101' which isn't there. 'SE-52' has the best regression model
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93 # of the available columns
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94 match = library_lookup._preferred(hits, ['OV-101'], column_type, polarity, model, method)
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95 expected = (['C150867', '(E)-phytol', 'C20H40O', 2158.5769891569125, 'Capillary',
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96 'Semi-standard non-polar', 'SE-52', '', 'C150867_SE-52', '', '', ''], 'SE-52')
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97 self.assertEqual(expected, match)
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98
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99 def test_format_result(self):
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100 '''
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101 Tests the 'format_result' function
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102 '''
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103 column_type = 'Capillary'
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104 polarity = 'Semi-standard non-polar'
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105
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106 # Look for DB-5
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107 pref_column = ['DB-5']
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108 model, method = library_lookup._read_model(self.ridb_poly_regress)
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109 lookup_dict = library_lookup.create_lookup_table(self.ri_database, column_type, polarity)
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110 data = library_lookup.format_result(lookup_dict, self.nist_output, pref_column, column_type,
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111 polarity, model, method)#False, None)
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112
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113 # remove non-hits from set:
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114 data = _get_hits_only(data)
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115 self.assertEqual(['C544354', 'Ethyl linoleate', 'C20H36O2', '2155', 'Capillary', 'Semi-standard non-polar',
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116 'DB-5', '1', 'C544354_DB-5', '1810', 'None', '', '', '0'], data[20])
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117 self.assertEqual(111, len(data))
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118
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119 # Look for both DB-5 and HP-5
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120 pref_column = ['DB-5', 'HP-5']
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121 data = library_lookup.format_result(lookup_dict, self.nist_output, pref_column, column_type,
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122 polarity, False, None)
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123 # remove non-hits from set:
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124 data = _get_hits_only(data)
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125 self.assertEqual(['C502614', '.beta.-(E)-Farnesene', 'C15H24', '1508', 'Capillary', 'Semi-standard non-polar',
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126 'DB-5', '1', 'C502614_DB-5', '942', 'None', '1482', '1522', '22'], data[50])
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127 self.assertEqual(106, len(data))
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128
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129
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130 def test_save_data(self):
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131 '''
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132 Tests the creation of the output tabular file
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133 '''
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134 temp_folder = tempfile.mkdtemp(prefix='gcms_combine_output_')
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135 saved_data = '{0}/{1}'.format(temp_folder, 'output.tsv')
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136 column_type = 'Capillary'
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137 polarity = 'Semi-standard non-polar'
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138 pref_column = ['DB-5']
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139 lookup_dict = library_lookup.create_lookup_table(self.ri_database, column_type, polarity)
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140 data = library_lookup.format_result(lookup_dict, self.nist_output, pref_column, column_type, polarity, False, None)
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141 library_lookup._save_data(data, saved_data)
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142 self.failUnless(os.path.exists(saved_data))
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143 shutil.rmtree(temp_folder)
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144
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145
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146 def test_match_library_get_lib_files(self):
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147 '''
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148 Tests the match_library.py functionality
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149 '''
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150 riqc_libs_dir = resource_filename(__name__, "../repositories")
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151 get_library_files_output = match_library.get_directory_files(riqc_libs_dir)
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152 self.assertEqual(4, len(get_library_files_output))
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153 self.assertEqual("Library_RI_DB_capillary_columns-noDuplicates", get_library_files_output[0][0])
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154 #TODO change assert below to assert that the result is a file, so the test can run on other dirs as well:
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155 #self.assertEqual("E:\\workspace\\PRIMS-metabolomics\\python-tools\\tools\\GCMS\\test\\data\\riqc_libs\\RI DB library (capillary columns) Dec.2012.txt", get_library_files_output[0][1])
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156 #self.assertEqual("RI DB library (capillary columns) Jan.2013", get_library_files_output[1][0])
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157 try:
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158 get_library_files_output = match_library.get_directory_files("/blah")
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159 # should not come here
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160 self.assertTrue(False)
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161 except:
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162 # should come here
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163 self.assertTrue(True)
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164
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165 def _get_hits_only(data):
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166 '''
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167 removes items that have RI == 0.0 and Name == '' (these are dummy lines just for the output
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168 '''
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169 result = []
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170 for item_idx in xrange(len(data)):
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171 item = data[item_idx]
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172 if item[1] != '' and item[3] > 0.0 :
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173 result.append(item)
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174
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175 return result
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176
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177
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178 if __name__ == "__main__":
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179 #import sys;sys.argv = ['', 'Test.testName']
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180 unittest.main()
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