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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 from shutil import rmtree
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6
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7
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8 class Test_F_LaunchRefAlign(unittest.TestCase):
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9
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10 def setUp(self):
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11 self._curTestDir = os.getcwd()
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12 self._testPrefix = 'test_LRA'
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13 try:
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14 os.makedirs(self._testPrefix)
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15 except:pass
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16 os.chdir(self._testPrefix)
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17
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18
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19 self._inputFastaFileName = "%s_input.fa" % self._testPrefix
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20 self._obsOutputFileName = self._inputFastaFileName +'.fa_aln'
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21 self._expOutputFileName = "%s_exp.fa_aln" % self._testPrefix
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22 self._writeInputFile()
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23
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24 def tearDown(self):
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25 os.chdir(self._curTestDir)
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26 try:
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27 rmtree(self._testPrefix)
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28 except:pass
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29
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30 def test_run(self):
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31 self._writeExpOutputFile_wo_refseq()
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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_KeepRefSeq(self):
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37 self._writeExpOutputFile_with_refseq()
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38 ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5, keepRefseq=True)
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39 ilauncher.run()
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40
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41 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
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42
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43 def test_run_as_script(self):
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44 self._writeExpOutputFile_wo_refseq()
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45 cmd = 'LaunchRefAlign.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
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46 os.system(cmd)
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47 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
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48
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49 def test_run_as_script_KeepRefSeq(self):
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50 self._writeExpOutputFile_with_refseq()
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51 cmd = 'LaunchRefAlign.py -i %s -r -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
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52 os.system(cmd)
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53 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
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54
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55 def _writeInputFile(self):
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56 InputFile = open(self._inputFastaFileName, 'w')
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57 InputFile.write('>sequence\n')
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58 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
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59 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
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60 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
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61 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
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62 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
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63 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
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64 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
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65 InputFile.write('>sequence2\n')
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66 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
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67 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
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68 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
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69 InputFile.close()
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70
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71 def _writeExpOutputFile_wo_refseq(self):
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72 with open(self._expOutputFileName,'w') as expOutputFile:
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73 expOutputFile.write(""">sequence2
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74 GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC
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75 GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT
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76 GCCTGTGTCTCTTCTCTC------------------------------------------
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77 ------------------------------------------------------------
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78 ----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------
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79 ------------------------------------------------------------
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80 -----------
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81 """)
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82
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83 def _writeExpOutputFile_with_refseq(self):
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84 with open(self._expOutputFileName,'w') as expOutputFile:
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85 expOutputFile.write(""">sequence
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86 GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC
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87 GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT
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88 GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA
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89 TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA
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90 TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC
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91 CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCAAGCGGTAGAAAGTGAG
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92 TGAGTGAGTGA
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93 >sequence2
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94 GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC
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95 GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT
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96 GCCTGTGTCTCTTCTCTC------------------------------------------
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97 ------------------------------------------------------------
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98 ----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------
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99 ------------------------------------------------------------
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100 -----------
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101 """)
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102
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103 if __name__ == "__main__":
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104 unittest.main() |
