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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.LaunchRefAlign import LaunchRefAlign
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5
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6
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7 class Test_F_LaunchRefAlign(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._obsOutputFileName = "obs"
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12 self._expOutputFileName = "exp"
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13 self._writeInputFile()
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14 self._writeExpOutputFile()
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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._expOutputFileName)
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23 # except:pass
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24 # try:
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25 # os.remove(self._obsOutputFileName)
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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 = LaunchRefAlign(self._inputFastaFileName,verbosity=5)
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33 ilauncher.run()
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34 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
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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
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42 def _writeInputFile(self):
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43 InputFile = open(self._inputFastaFileName, 'w')
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44 InputFile.write('>sequence\n')
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45 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
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46 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
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47 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
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48 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
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49 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
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50 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
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51 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
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52 InputFile.write('>sequence2\n')
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53 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
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54 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
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55 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
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56 InputFile.close()
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57
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58 def _writeExpOutputFile(self):
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59 with open(self._expOutputFileName,'w') as expOutputFile:
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60 expOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21
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61 2\t(GGT)5\tsequence\t10\t23
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62 3\t(GTGTGA)4\tsequence\t222\t242
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63 4\t(GTCCA)2\tsequence\t282\t292
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64 5\t(AGTG)4\tsequence\t355\t371
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65 6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152
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66 7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151
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67 8\t(TC)23\tsequence2\t107\t152
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68 """)
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69
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70
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71 if __name__ == "__main__":
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72 unittest.main() |
