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1 import unittest
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4 from commons.launcher.LaunchTRF import LaunchTRF
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5
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6
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7 class Test_F_LaunchTRF(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._inputFastaFileName = "input.fa"
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11 self._obsTRFOutputFileName = "obsTRF.TRF.set"
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12 self._expTRFOutputFileName = "expTRF.TRF.set"
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13 self._writeInputFile()
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14 self._writeExpTRFOutputFile()
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15
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16 def tearDown(self):
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17 try:
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18 os.remove(self._inputFastaFileName)
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19 except:pass
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20
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21 try:
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22 os.remove(self._expTRFOutputFileName)
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23 except:pass
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24 try:
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25 os.remove(self._obsTRFOutputFileName)
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26 except:pass
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27 try:
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28 os.remove("input.fa.2.3.5.80.10.20.15.dat")
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29 except:pass
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30
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31 def test_run(self):
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32 ilauncher = LaunchTRF(self._inputFastaFileName,self._obsTRFOutputFileName,verbosity=5)
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33 ilauncher.run()
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34 self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))
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35
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36 def test_run_as_script(self):
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37 cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName)
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38 os.system(cmd)
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39 self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))
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40
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41 def test_run_as_scriptNoOutputGiven(self):
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42 cmd = 'LaunchTRF.py -i %s -v 3' % (self._inputFastaFileName)
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43 os.system(cmd)
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44 self._obsTRFOutputFileName = "input.fa.TRF.set"
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45 self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))
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46
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47 def test_run_as_scriptNoOutputGivenDoClean(self):
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48 cmd = 'LaunchTRF.py -i %s -c -v 3' % (self._inputFastaFileName)
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49 os.system(cmd)
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50 self._obsTRFOutputFileName = "input.fa.TRF.set"
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51 datFilePath = os.path.join(os.getcwd(),"%s.2.3.5.80.10.20.15.dat" % self._inputFastaFileName)
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52 self.assertFalse(os.path.exists(datFilePath))
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53
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54 def _writeInputFile(self):
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55 InputFile = open(self._inputFastaFileName, 'w')
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56 InputFile.write('>sequence\n')
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57 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
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58 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
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59 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
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60 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
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61 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
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62 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
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63 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
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64 InputFile.write('>sequence2\n')
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65 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
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66 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
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67 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
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68 InputFile.close()
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69
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70 def _writeExpTRFOutputFile(self):
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71 with open(self._expTRFOutputFileName,'w') as expTRFOutputFile:
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72 expTRFOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21
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73 2\t(GGT)5\tsequence\t10\t23
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74 3\t(GTGTGA)4\tsequence\t222\t242
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75 4\t(GTCCA)2\tsequence\t282\t292
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76 5\t(AGTG)4\tsequence\t355\t371
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77 6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152
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78 7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151
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79 8\t(TC)23\tsequence2\t107\t152
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80 """)
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81
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82
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83 if __name__ == "__main__":
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84 unittest.main() |
