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1 import unittest
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2 import os
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3 import time
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4 from commons.core.coord.Align import Align
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5 from commons.core.utils.FileUtils import FileUtils
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6 from commons.tools.RmvPairAlignInChunkOverlaps import RmvPairAlignInChunkOverlaps
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7
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8
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9 class Test_RmvPairAlignInChunkOverlaps( unittest.TestCase ):
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10
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11 def setUp( self ):
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12 self._i = RmvPairAlignInChunkOverlaps()
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13 self._uniqId = "%s" % ( time.strftime("%Y%m%d%H%M%S") )
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14
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15
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16 def tearDown( self ):
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17 self._i = None
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18 self._uniqId = None
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19
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20
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21 def test_isPairAlignAChunkOverlap( self ):
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22 a = Align()
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23 a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "100", "0.0", "125", "97.6" ) )
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24 self._i.setChunkLength( 500 )
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25 self._i.setChunkOverlap( 100 )
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26 obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
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27 self.assertTrue( obs )
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28 a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "100", "0.0", "125", "97.6" ) ) # reverse subject
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29 obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
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30 self.assertTrue( obs )
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31 a.setFromTuple( ( "chunk1", "401", "500", "chunk3", "1", "100", "0.0", "125", "97.6" ) ) # chunk subject not contiguous
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32 obs = self._i.isPairAlignAChunkOverlap( a, 1, 3 )
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33 self.assertFalse( obs )
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34 a.setFromTuple( ( "chunk1", "390", "500", "chunk2", "1", "110", "0.0", "125", "97.6" ) ) # hit longer than chunk overlap
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35 obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
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36 self.assertFalse( obs )
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37 a.setFromTuple( ( "chunk2", "1", "101", "chunk1", "401", "500", "0.0", "500", "100.0" ) ) # chunk overlap returned by PALS (+1), query > subject
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38 obs = self._i.isPairAlignAChunkOverlap( a, 2, 1 )
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39 self.assertTrue( obs )
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40 a.setFromTuple( ( "chunk1", "401", "500", "chunk2", "1", "101", "0.0", "500", "100.0" ) ) # chunk overlap returned by PALS (+1), query < subject
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41 obs = self._i.isPairAlignAChunkOverlap( a, 1, 2 )
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42 self.assertTrue( obs )
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43
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44
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45 def test_isPairAlignWithinAndDueToAChunkOverlap( self ):
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46 a = Align()
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47 a.setFromTuple( ( "chunk1", "411", "450", "chunk2", "11", "50", "0.0", "73", "97.6" ) ) # included, due to overlap
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48 self._i.setChunkLength( 500 )
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49 self._i.setChunkOverlap( 100 )
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50 self._i._verbose = 0
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51 obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
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52 self.assertTrue( obs )
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53 a.setFromTuple( ( "chunk1", "411", "450", "chunk2", "50", "11", "0.0", "73", "97.6" ) ) # reverse subject
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54 obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
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55 self.assertFalse( obs )
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56 a.setFromTuple( ( "chunk1", "401", "500", "chunk3", "1", "100", "0.0", "125", "97.6" ) ) # chunk subject not contiguous
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57 obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 3 )
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58 self.assertFalse( obs )
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59 a.setFromTuple( ( "chunk1", "390", "500", "chunk2", "1", "110", "0.0", "125", "97.6" ) ) # hit longer than chunk overlap
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60 obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
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61 self.assertFalse( obs )
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62 a.setFromTuple( ( "chunk1", "411", "430", "chunk2", "16", "35", "0.0", "73", "97.6" ) ) # repeat within overlap...
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63 self._i._margin = 2 # ... but not due to it
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64 obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
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65 self.assertFalse( obs )
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66 self._i._margin = 10 # ... and due to it
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67 obs = self._i.isPairAlignWithinAndDueToAChunkOverlap( a, 1, 2 )
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68 self.assertTrue( obs )
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69
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70
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71 def test_removeChunkOverlaps( self ):
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72 inFileName = "dummyInFile_%s" % ( self._uniqId )
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73 inF = open( inFileName, "w" )
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74 a = Align()
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75 a.setFromTuple( ( "chunk1", "411", "490", "chunk2", "11", "90", "0.0", "73", "97.6" ) )
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76 a.write( inF )
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77 a.setFromTuple( ( "chunk1", "1", "500", "chunk1", "1", "500", "0.0", "500", "100.0" ) )
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78 a.write( inF )
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79 inF.close()
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80 self._i.setInputFileName( inFileName )
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81 self._i.setChunkLength( 500 )
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82 self._i.setChunkOverlap( 100 )
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83 obsFileName = "dummyObsFile_%s" %( self._uniqId )
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84 self._i.setOutputFileName( obsFileName )
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85 d = self._i.removeChunkOverlaps()
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86 expFileName = "dummyExpFile_%s" % ( self._uniqId )
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87 expF = open( expFileName, "w" )
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88 expF.write( "" )
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89 expF.close()
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90 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
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91 for f in [ inFileName, obsFileName, expFileName ]: os.remove( f )
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92
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93
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94 def test_zRunAsScript( self ):
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95 cDir = os.getcwd()
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96
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97 alignFileName = "dummyInFile_%s" % ( self._uniqId )
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98 aF = open( alignFileName, "w" )
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99 aF.write( "chunk1\t401\t500\tchunk2\t1\t100\t0.0\t131\t100.0\n" ) # remove
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100 aF.write( "chunk2\t1\t100\tchunk1\t401\t500\t0.0\t132\t100.0\n" ) # remove
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101 aF.write( "chunk1\t401\t500\tchunk3\t1\t100\t0.0\t132\t100.0\n" ) # keep because non-contiguous chunks
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102 aF.write( "chunk3\t401\t500\tchunk1\t1\t100\t0.0\t132\t100.0\n" ) # keep because non-contiguous chunks
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103 aF.write( "chunk1\t401\t500\tchunk2\t100\t1\t0.0\t132\t100.0\n" ) # keep because within overlap but reverse
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104 aF.write( "chunk1\t431\t490\tchunk2\t31\t90\t0.0\t132\t100.0\n" ) # remove because within and due to overlap
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105 aF.write( "chunk1\t411\t430\tchunk2\t61\t90\t0.0\t132\t100.0\n" ) # keep because within but not due to overlap
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106 aF.write( "chunk1\t390\t500\tchunk2\t1\t100\t0.0\t132\t100.0\n" ) # keep because longer HSP on query
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107 aF.close()
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108
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109 expFileName = "dummyExpFile_%s" % ( self._uniqId )
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110 expF = open( expFileName, "w" )
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111 expF.write( "chunk1\t401\t500\tchunk3\t1\t100\t0\t132\t100.000000\n" )
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112 expF.write( "chunk3\t401\t500\tchunk1\t1\t100\t0\t132\t100.000000\n" )
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113 expF.write( "chunk1\t401\t500\tchunk2\t100\t1\t0\t132\t100.000000\n" )
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114 expF.write( "chunk1\t411\t430\tchunk2\t61\t90\t0\t132\t100.000000\n" )
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115 expF.write( "chunk1\t390\t500\tchunk2\t1\t100\t0\t132\t100.000000\n" )
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116 expF.close()
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117
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118 obsFileName = "dummyObsFile_%s" % ( self._uniqId )
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119 cmd = "RmvPairAlignInChunkOverlaps.py"
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120 cmd += " -i %s" % ( alignFileName )
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121 cmd += " -l 500"
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122 cmd += " -o 100"
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123 cmd += " -O %s" % ( obsFileName )
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124 cmd += " -v 0"
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125 os.system( cmd )
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126
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127 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
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128 for f in [ alignFileName, expFileName, obsFileName ]: os.remove( f )
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129 os.chdir( cDir )
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130
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131 def test_zRunAsScript_bug_to_fix(self):
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132 cDir = os.getcwd()
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133
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134 alignFileName = "dummyInFile_%s" % ( self._uniqId )
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135 aF = open( alignFileName, "w" )
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136 aF.write("chunk4\t63217\t63680\tchunk5\t195316\t194837\t0\t676\t92.71\n")
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137 aF.write("chunk4\t63217\t63680\tchunk6\t2618\t3101\t0\t714\t93.6\n")
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138 aF.write("chunk4\t63217\t63680\tchunk6\t5316\t4837\t0\t676\t92.71\n")
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139 aF.close()
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140
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141 expFileName = "dummyExpFile_%s" % ( self._uniqId )
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142 expF = open( expFileName, "w" )
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143 expF.write("chunk4\t63217\t63680\tchunk5\t195316\t194837\t0\t676\t92.71\n")
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144 expF.write("chunk4\t63217\t63680\tchunk6\t2618\t3101\t0\t714\t93.6\n")
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145 expF.close()
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146
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147 obsFileName = "dummyObsFile_%s" % ( self._uniqId )
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148 cmd = "RmvPairAlignInChunkOverlaps.py"
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149 cmd += " -i %s" % ( alignFileName )
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150 cmd += " -l 200000"
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151 cmd += " -o 10000"
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152 cmd += " -O %s" % ( obsFileName )
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153 cmd += " -v 0"
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154 os.system( cmd )
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155
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156 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
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157 for f in [ alignFileName, expFileName, obsFileName ]: os.remove( f )
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158 os.chdir( cDir )
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159
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160 if __name__ == "__main__":
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161 unittest.main() |
