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1 import os
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2 import unittest
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3 from commons.core.utils.FileUtils import FileUtils
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4 from devTools.tests.MockFastaSupctg30 import MockFastaSupctg30
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5 from devTools.tests.MockMiniProtBankSupctg30 import MockMiniProtBankSupctg30
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6 from commons.launcher.tests.MockDataBankForBlat import MockDataBankForBlat
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7 from commons.launcher.tests.MockESTBankForBlat import MockESTBankForBlat
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8 from commons.launcher.tests.MockOutputForBlat import MockOutputForBlat
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9 from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
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10
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11 class Test_F_BlatProgramLauncher(unittest.TestCase):
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12
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13 def test_run_empty_result(self):
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14 queryFileName = "smallProtBank_supctg30.fa"
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15 mock = MockMiniProtBankSupctg30()
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16 mock.write(queryFileName)
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17 subjectFileName = "subjectBank.fa"
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18 mock = MockFastaSupctg30()
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19 mock.write(subjectFileName)
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20
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21 expOutputFileName = "expBlatOutput.blast.align"
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22 self.writeEmptyExpOutputFile(expOutputFileName)
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23
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24 obsOutputFileName = "obsBlatOutput.blast.align"
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25
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26 bpl = BlatProgramLauncher()
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27 bpl.setInputFile(queryFileName)
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28 bpl.setSubjectFile(subjectFileName)
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29 bpl.setOutputFile(obsOutputFileName)
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30 bpl.setProgramParameters("")
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31 bpl.run()
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32
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33 blastFileName = queryFileName + ".blast"
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34
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35 self.assertTrue(os.path.exists(obsOutputFileName))
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36 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
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37
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38 os.remove(queryFileName)
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39 os.remove(subjectFileName)
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40 os.remove(blastFileName)
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41 os.remove(expOutputFileName)
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42 os.remove(obsOutputFileName)
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43
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44 def test_as_script_empty_result(self):
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45 queryFileName = "smallProtBank_supctg30.fa"
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46 mock = MockMiniProtBankSupctg30()
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47 mock.write(queryFileName)
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48 subjectFileName = "subjectBank.fa"
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49 mock = MockFastaSupctg30()
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50 mock.write(subjectFileName)
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51
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52 expOutputFileName = "expBlatOutput.blast.align"
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53 self.writeEmptyExpOutputFile(expOutputFileName)
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54
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55 obsOutputFileName = "obsBlatOutput.blast.align"
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56
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57 cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
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58
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59 os.system(cmd2Launch)
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60
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61 blastFileName = queryFileName + ".blast"
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62
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63 self.assertTrue(os.path.exists(obsOutputFileName))
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64 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
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65
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66 os.remove(queryFileName)
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67 os.remove(subjectFileName)
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68 os.remove(blastFileName)
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69 os.remove(expOutputFileName)
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70 os.remove(obsOutputFileName)
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71
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72 def test_run(self):
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73 queryFileName = "smallESTBank.fa"
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74 mock = MockESTBankForBlat()
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75 mock.write(queryFileName)
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76 subjectFileName = "subjectBank.fa"
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77 mock = MockDataBankForBlat()
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78 mock.write(subjectFileName)
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79
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80 expOutputFileName = "expBlatOutput.blast.align"
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81 mock = MockOutputForBlat()
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82 mock.write(expOutputFileName)
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83
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84 obsOutputFileName = "obsBlatOutput.blast.align"
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85
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86 bpl = BlatProgramLauncher()
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87 bpl.setInputFile(queryFileName)
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88 bpl.setSubjectFile(subjectFileName)
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89 bpl.setOutputFile(obsOutputFileName)
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90 bpl.setProgramParameters("")
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91 bpl.run()
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92
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93 blastFileName = queryFileName + ".blast"
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94
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95 self.assertTrue(os.path.exists(obsOutputFileName))
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96 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
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97
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98 os.remove(queryFileName)
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99 os.remove(subjectFileName)
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100 os.remove(blastFileName)
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101 os.remove(expOutputFileName)
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102 os.remove(obsOutputFileName)
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103
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104 def test_as_script(self):
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105 queryFileName = "smallESTBank.fa"
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106 mock = MockESTBankForBlat()
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107 mock.write(queryFileName)
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108 subjectFileName = "subjectBank.fa"
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109 mock = MockDataBankForBlat()
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110 mock.write(subjectFileName)
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111
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112 expOutputFileName = "expBlatOutput.blast.align"
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113 mock = MockOutputForBlat()
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114 mock.write(expOutputFileName)
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115
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116 obsOutputFileName = "obsBlatOutput.blast.align"
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117
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118 cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
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119
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120 os.system(cmd2Launch)
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121
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122 blastFileName = queryFileName + ".blast"
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123
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124 self.assertTrue(os.path.exists(obsOutputFileName))
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125 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
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126
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127 os.remove(queryFileName)
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128 os.remove(subjectFileName)
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129 os.remove(blastFileName)
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130 os.remove(expOutputFileName)
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131 os.remove(obsOutputFileName)
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132
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133 def writeEmptyExpOutputFile(self, outputFileName):
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134 f = open(outputFileName, "w")
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135 f.write("")
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136 f.close()
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137
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138 if __name__ == "__main__":
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139 unittest.main() |
