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1 import unittest
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2 from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher
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3
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4
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5 class Test_RepeatMaskerProgramLauncher( unittest.TestCase ):
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6
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7 def setUp( self ):
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8 self._i = RepeatMaskerProgramLauncher()
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9
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10
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11 def tearDown( self ):
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12 self._i = None
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13
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14
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15 def test_getSpecificHelpAsString( self ):
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16 exp = ""
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17 exp += "\nspecific options:"
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18 exp += "\n -s: name of the subject file (repeats, format='fasta')"
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19 exp += "\n -n: nb of processors to use in parallel (default='%i')" % ( self._i.getNbProcessors() )
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20 exp += "\n -g: calculate the GC content"
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21 exp += "\n -b: skip bacterial insertion element check"
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22 exp += "\n -l: does not mask low-complexity DNA or simple repeats"
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23 exp += "\n -m: only masks low complex/simple repeats (no interspersed repeats)"
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24 exp += "\n -o: name of the output file"
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25 exp += "\n with -s: format='align', default=inFile+'.cat.align')"
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26 exp += "\n with -m: format='path', default=inFile+'.cat.path')"
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27 obs = self._i.getSpecificHelpAsString()
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28 self.assertEqual( exp, obs )
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29
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30
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31 def test_setASpecificAttributeFromCmdLine( self ):
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32 self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
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33 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
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34
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35 self._i.setASpecificAttributeFromCmdLine( "-n", "2" )
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36 self.assertEqual( 2, self._i.getNbProcessors() )
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37
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38 self._i.setASpecificAttributeFromCmdLine( "-g" )
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39 self.assertEqual( True, self._i.getCalculateGCcontent() )
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40
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41 self._i.setASpecificAttributeFromCmdLine( "-b" )
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42 self.assertEqual( True, self._i.getSkipBacterialIsCheck() )
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43
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44 self._i.setASpecificAttributeFromCmdLine( "-l" )
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45 self.assertEqual( False, self._i.getMaskSsr() )
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46
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47 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
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48 self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
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49
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50
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51 def test_setWrapperCommandLine( self ):
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52 self._i.setInputFile( "dummyInFile.fa" )
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53 self._i.setSubjectFile( "dummySubjectFile.fa" )
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54 exp = "RepeatMaskerProgramLauncher.py"
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55 exp += " -i %s" % ( "dummyInFile.fa" )
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56 exp += " -s %s" % ( "dummySubjectFile.fa" )
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57 exp += " -n 1"
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58 self._i.setWrapperCommandLine()
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59 obs = self._i.getWrapperCommandLine()
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60 self.assertEqual( exp, obs )
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61
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62
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63 def test_setProgramCommandLine( self ):
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64 self._i.setInputFile( "dummyInFile.fa" )
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65 self._i.setSubjectFile( "dummySubjectFile.fa" )
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66 self._i.setCalculateGCcontent()
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67 self._i.setSkipBacterialIsCheck()
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68 exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow -lib dummySubjectFile.fa dummyInFile.fa"
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69 self._i.setProgramCommandLine()
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70 obs = self._i.getProgramCommandLine()
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71 self.assertEqual( exp, obs )
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72
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73
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74 def test_setProgramCommandLine_withoutSubjects_withMaskSsr( self ):
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75 self._i.setInputFile( "dummyInFile.fa" )
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76 self._i.setCalculateGCcontent()
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77 self._i.setSkipBacterialIsCheck()
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78 exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow dummyInFile.fa"
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79 self._i.setProgramCommandLine()
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80 obs = self._i.getProgramCommandLine()
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81 self.assertEqual( exp, obs )
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82
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83
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84 def test_setListFilesToKeep_onlyInFile( self ):
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85 self._i.setInputFile( "dummyInFile.fa" )
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86 self._i.setOnlySsr()
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87 lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.path" ]
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88 self._i.setListFilesToKeep()
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89 lObs = self._i.getListFilesToKeep()
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90 lExp.sort()
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91 lObs.sort()
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92 self.assertEqual( lExp, lObs )
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93
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94
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95 def test_setListFilesToKeep_withSubjectFile( self ):
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96 self._i.setInputFile( "dummyInFile.fa" )
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97 self._i.setSubjectFile( "dummySbjFile.fa" )
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98 lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.align" ]
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99 self._i.setListFilesToKeep()
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100 lObs = self._i.getListFilesToKeep()
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101 lExp.sort()
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102 lObs.sort()
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103 self.assertEqual( lExp, lObs )
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104
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105
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106 def test_setListFilesToKeep_inFileAndOutFile( self ):
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107 self._i.setInputFile( "dummyInFile.fa" )
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108 self._i.setOutputFile( "dummyOutFile.align" )
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109 lExp = [ "dummyInFile.fa.cat", "dummyOutFile.align" ]
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110 self._i.setListFilesToKeep()
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111 lObs = self._i.getListFilesToKeep()
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112 lExp.sort()
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113 lObs.sort()
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114 self.assertEqual( lExp, lObs )
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115
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116
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117 def test_setListFilesToKeep_inFileAndOutFileAndSsr( self ):
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118 self._i.setInputFile( "dummyInFile.fa" )
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119 self._i.unsetMaskSsr()
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120 self._i.setOutputFile( "dummyOutFile.path" )
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121 lExp = [ "dummyInFile.fa.cat", "dummyOutFile.path" ]
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122 self._i.setListFilesToKeep()
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123 lObs = self._i.getListFilesToKeep()
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124 lExp.sort()
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125 lObs.sort()
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126 self.assertEqual( lExp, lObs )
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127
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128
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129 def test_setListFilesToRemove( self ):
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130 self._i.setInputFile( "dummyInFile.fa" )
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131 lExp = [ "dummyInFile.fa.out", \
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132 "dummyInFile.fa.log", \
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133 "dummyInFile.fa.stderr", \
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134 "dummyInFile.fa.ori.out", \
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135 "dummyInFile.fa.masked", \
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136 "dummyInFile.fa.tbl", \
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137 "dummyInFile.fa.ref" ]
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138 self._i.setListFilesToRemove()
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139 lObs = self._i.getListFilesToRemove()
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140 lExp.sort()
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141 lObs.sort()
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142 self.assertEqual( lExp, lObs )
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143
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144
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145 def test_setSummary( self ):
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146 self._i.setInputFile( "dummyInFile.fa" )
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147 self._i.setSubjectFile( "dummySubjectFile.fa" )
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148 exp = "input file: %s" % ( self._i.getInputFile() )
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149 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
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150 exp += "\nnb processors: %i" % ( self._i.getNbProcessors() )
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151 exp += "\nmask low-complexity DNA or simple repeats"
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152 exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.path" )
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153 self._i.setSummary()
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154 obs = self._i.getSummary()
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155 self.assertEqual( exp, obs )
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156
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157
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158 def test_setSummary_noMaskSsr( self ):
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159 self._i.setInputFile( "dummyInFile.fa" )
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160 self._i.setSubjectFile( "dummySubjectFile.fa" )
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161 self._i.unsetMaskSsr()
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162 exp = "input file: %s" % ( self._i.getInputFile() )
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163 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
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164 exp += "\nnb processors: %i" % ( self._i.getNbProcessors() )
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165 exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.align" )
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166 self._i.setSummary()
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167 obs = self._i.getSummary()
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168 self.assertEqual( exp, obs )
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169
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170 if __name__ == "__main__":
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171 unittest.main() |