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1 import os
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2 import sys
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3 import unittest
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4 from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFasta
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5 from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFastq
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6 from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionExpectedCSV
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7
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8 class Test_F_getLetterDistribution(unittest.TestCase):
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9
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10 def tearDown(self):
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11 os.system("rm tmp*.*")
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12
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13 def test_getLetterDistributionWithFasta(self):
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14 iFastaMock = MockGetLetterDistributionFasta()
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15 fastaFileName = "MockFasta_GetLetterDistribution.fa"
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16 iFastaMock.write(fastaFileName)
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17
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18 outputName = "dummy_result_fasta"
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19 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s" % (os.environ["REPET_PATH"], fastaFileName, outputName))
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20
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21 self.assertTrue (os.path.exists(outputName + ".png"))
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22 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
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23
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24 os.remove(outputName + ".png")
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25 os.remove(outputName + "PerNt.png")
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26 os.remove(fastaFileName)
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27
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28 def test_getLetterDistributionWithFastq(self):
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29 iFastqMock = MockGetLetterDistributionFastq()
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30 fastqFileName = "MockFastq_GetLetterDistribution.fastq"
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31 iFastqMock.write(fastqFileName)
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32
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33 outputName = "dummy_result_fastq"
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34 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s" % (os.environ["REPET_PATH"], fastqFileName, outputName))
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35
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36 self.assertTrue (os.path.exists(outputName + ".png"))
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37 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
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38
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39 os.remove(fastqFileName)
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40 os.remove(outputName + ".png")
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41 os.remove(outputName + "PerNt.png")
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42
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43 def test_getLetterDistributionWithFastaCSVOutput(self):
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44 iFastaMock = MockGetLetterDistributionFasta()
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45 fastaFileName = "MockFasta_GetLetterDistribution.fa"
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46 iFastaMock.write(fastaFileName)
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47
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48 iCSVMock = MockGetLetterDistributionExpectedCSV()
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49 expCSVFileName = "expCSV.csv"
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50 iCSVMock.write(expCSVFileName)
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51
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52 outputName = "dummy_result_fasta"
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53 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s -c" % (os.environ["REPET_PATH"], fastaFileName, outputName))
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54
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55 obsCSVFileName = outputName + ".csv"
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56
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57 self.assertTrue (os.path.exists(outputName + ".png"))
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58 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
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59 self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
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60
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61 os.remove(outputName + ".png")
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62 os.remove(outputName + "PerNt.png")
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63 os.remove(fastaFileName)
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64 os.remove(expCSVFileName)
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65 os.remove(obsCSVFileName)
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66
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67 def test_getLetterDistributionWithFastqCVSOutput(self):
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68 iFastqMock = MockGetLetterDistributionFastq()
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69 fastqFileName = "MockFastq_GetLetterDistribution.fastq"
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70 iFastqMock.write(fastqFileName)
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71
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72 iCSVMock = MockGetLetterDistributionExpectedCSV()
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73 expCSVFileName = "expCSV.csv"
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74 iCSVMock.write(expCSVFileName)
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75
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76 outputName = "dummy_result_fastq"
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77 os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s -c" % (os.environ["REPET_PATH"], fastqFileName, outputName))
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78
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79 obsCSVFileName = outputName + ".csv"
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80
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81 self.assertTrue (os.path.exists(outputName + ".png"))
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82 self.assertTrue (os.path.exists(outputName + "PerNt.png"))
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83 self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
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84
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85 os.remove(fastqFileName)
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86 os.remove(outputName + ".png")
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87 os.remove(outputName + "PerNt.png")
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88 os.remove(expCSVFileName)
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89 os.remove(obsCSVFileName)
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90
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91 def _are2FilesIdentical(self, file1, file2 ):
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92 tmpFile = "diff_%s_%s" % ( os.path.basename(file1), os.path.basename(file2) )
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93 cmd = "diff %s %s >> %s" % ( file1, file2, tmpFile )
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94 returnStatus = os.system( cmd )
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95 if returnStatus != 0:
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96 msg = "ERROR: 'diff' returned '%i'" % ( returnStatus )
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97 sys.stderr.write( "%s\n" % msg )
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98 sys.stderr.flush()
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99 os.remove( tmpFile )
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100 return False
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101 if self.isEmpty( tmpFile ):
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102 os.remove( tmpFile )
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103 return True
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104 else:
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105 os.remove( tmpFile )
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106 return False
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107
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108 def getNbLinesInSingleFile(self, fileName):
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109 fileHandler = open(fileName, "r" )
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110 lines = fileHandler.readlines()
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111 fileHandler.close()
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112 return len(lines)
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113
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114 def isEmpty(self, fileName):
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115 return 0 == self.getNbLinesInSingleFile( fileName )
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116
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117 if __name__ == "__main__":
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118 unittest.main()
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