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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import unittest
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33 import os
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34 from commons.core.utils.FileUtils import FileUtils
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35 from commons.core.coord.MatchUtils import MatchUtils
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36 from commons.core.coord.Match import Match
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37 from commons.core.seq.BioseqDB import BioseqDB
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38
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39
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40 class Test_MatchUtils( unittest.TestCase ):
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41
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42 def test_getMatchListFromFile( self ):
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43 inFile = "dummyInFile"
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44 inFileHandler = open( inFile, "w" )
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45 inFileHandler.write( "query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n" )
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46 m1 = Match()
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47 m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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48 m1.write( inFileHandler )
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49 m2 = Match()
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50 m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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51 m2.write( inFileHandler )
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52 inFileHandler.close()
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53
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54 lExp = [ m1, m2 ]
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55
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56 lObs = MatchUtils.getMatchListFromFile( inFile )
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57
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58 self.assertEquals( lExp, lObs )
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59
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60 os.remove( inFile )
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61
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62 def test_getDictOfListsWithSubjectAsKey( self ):
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63 m1 = Match()
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64 m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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65 m2 = Match()
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66 m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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67 lMatch = [ m1, m2 ]
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68
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69 dExp = { "SName1": [ m1 ], "SName2": [ m2 ] }
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70
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71 dObs = MatchUtils.getDictOfListsWithSubjectAsKey( lMatch )
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72
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73 self.assertEquals( dExp, dObs )
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74
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75 def test_getDictOfListsWithQueryAsKey( self ):
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76 m1 = Match()
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77 m1.setFromTuple( ("QName1", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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78 m2 = Match()
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79 m2.setFromTuple( ("QName2", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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80 m3 = Match()
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81 m3.setFromTuple( ("QName1", 1, 5, 5, 0.1, 0.2, "SName3", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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82 lMatch = [ m1, m2, m3 ]
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83
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84 dExp = { "QName1": [ m1, m3 ], "QName2": [ m2 ] }
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85
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86 dObs = MatchUtils.getDictOfListsWithQueryAsKey( lMatch )
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87
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88 self.assertEquals( dExp, dObs )
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89
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90 def test_getIdListFromMatchList( self ):
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91 m1 = Match()
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92 m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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93 m2 = Match()
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94 m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) )
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95 lMatch = [ m1, m2 ]
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96
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97 lExp = [1, 10]
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98
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99 lObs = MatchUtils.getIdListFromMatchList( lMatch )
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100
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101 self.assertEquals(lExp, lObs)
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102
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103 def test_getIdListFromMatchList_empty_list( self ):
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104 lMatch = []
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105 lExp = []
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106
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107 lObs = MatchUtils.getIdListFromMatchList( lMatch )
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108
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109 self.assertEquals(lExp, lObs)
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110
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111 def test_writeListInFile_without_header( self ):
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112 m1 = Match()
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113 m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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114 m2 = Match()
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115 m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) )
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116 lMatch = [ m1, m2 ]
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117
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118 line1 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName1\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t1\n"
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119 line2 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName2\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t10\n"
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120
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121 expFileName = "expFileName.match"
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122 expFileHandle = open ( expFileName, 'w' )
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123 expFileHandle.write(line1)
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124 expFileHandle.write(line2)
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125 expFileHandle.close()
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126
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127 obsFileName = "obsFileName.match"
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128
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129 MatchUtils.writeListInFile( lMatch, obsFileName )
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130
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131 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
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132
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133 os.remove( obsFileName )
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134 os.remove( expFileName )
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135
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136 def test_writeListInFile_with_header( self ):
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137 m1 = Match()
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138 m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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139 m2 = Match()
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140 m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) )
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141 lMatch = [ m1, m2 ]
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142
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143 headerLine = "query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n"
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144
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145 line1 = headerLine
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146 line2 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName1\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t1\n"
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147 line3 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName2\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t10\n"
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148
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149 expFileName = "expFileName.match"
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150 expFileHandle = open ( expFileName, 'w' )
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151 expFileHandle.write(line1)
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152 expFileHandle.write(line2)
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153 expFileHandle.write(line3)
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154 expFileHandle.close()
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155
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156 obsFileName = "obsFileName.match"
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157
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158 MatchUtils.writeListInFile( lMatch, obsFileName, header=headerLine )
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159
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160 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
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161
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162 os.remove( obsFileName )
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163 os.remove( expFileName )
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164
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165 def test_writeListInFile_with_append_mode( self ):
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166 m1 = Match()
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167 m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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168 m2 = Match()
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169 m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) )
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170 lMatch = [ m1, m2 ]
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171
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172 line1 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName1\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t1\n"
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173 line2 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName2\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t10\n"
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174
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175 expFileName = "expFileName.match"
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176 expFileHandle = open ( expFileName, 'w' )
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177 expFileHandle.write(line1)
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178 expFileHandle.write(line1)
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179 expFileHandle.write(line2)
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180 expFileHandle.close()
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181
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182 obsFileName = "obsFileName.match"
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183 obsFileHandle = open ( obsFileName, 'w' )
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184 obsFileHandle.write(line1)
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185 obsFileHandle.close()
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186
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187 MatchUtils.writeListInFile( lMatch, obsFileName, 'a' )
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188
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189 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
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190
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191 os.remove( obsFileName )
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192 os.remove( expFileName )
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193
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194 def test_rmvDuplicateMatches(self):
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195 m1 = Match()
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196 m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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197 m2 = Match()
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198 m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 86.2, 1) )
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199 m3 = Match()
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200 m3.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) )
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201 lMatch = [ m1, m3, m2 ]
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202
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203 lExp = [m1, m2]
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204 lObs = MatchUtils.rmvDuplicateMatches(lMatch)
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205
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206 self.assertEquals(lExp, lObs)
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207
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208 def test_filterDiffQrySbj_same_seq(self):
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209 fastaFileName = "file.fa"
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210 self._writeFastaFile(fastaFileName)
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211 qryDB = BioseqDB(fastaFileName)
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212 tabFileName = "file.tab"
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213 self._writeMatchFile(tabFileName)
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214
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215 expListToKeep = ["HELITRON2"]
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216 obsListToKeep = MatchUtils.filterDiffQrySbj(qryDB,tabFileName, 0.95, 0.98, 2)
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217 self.assertEquals(expListToKeep, obsListToKeep)
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218 os.remove(fastaFileName)
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219 os.remove(tabFileName)
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220
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221 def test_filterDiffQrySbj_TE_included_in_67percent_in_other_TE(self):
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222 fastaFileName = "file.fa"
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223 self._writeFastaFile2(fastaFileName)
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224 qryDB = BioseqDB(fastaFileName)
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225 tabFileName = "file.tab"
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226 self._writeMatchFile2(tabFileName)
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227 expListToKeep = []
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228 obsListToKeep = MatchUtils.filterDiffQrySbj(qryDB, tabFileName, 0.95, 0.98, 2)
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229 self.assertEquals(expListToKeep, obsListToKeep)
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230 os.remove(fastaFileName)
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231 os.remove(tabFileName)
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232
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233 def test_getNbDistinctSequencesInsideMatchesWithThresh_query(self):
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234 tabFileName = "file.tab"
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235 self._writeMatchFile3(tabFileName)
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236 lMatches = MatchUtils.getMatchListFromFile(tabFileName)
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237 expNbDistinctMatches = 1
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238 obsNbDistinctMatches = MatchUtils.getNbDistinctSequencesInsideMatchesWithThresh(lMatches,0.95, 0.98,"query")
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239 self.assertEquals(expNbDistinctMatches, obsNbDistinctMatches)
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240 os.remove(tabFileName)
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241
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242 def test_getNbDistinctSequencesInsideMatchesWithThresh_subject(self):
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243 tabFileName = "file.tab"
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244 self._writeMatchFile3(tabFileName)
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245 lMatches = MatchUtils.getMatchListFromFile(tabFileName)
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246 expNbDistinctMatches = 1
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247 obsNbDistinctMatches = MatchUtils.getNbDistinctSequencesInsideMatchesWithThresh(lMatches,0.95, 0.98,"subject")
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248 self.assertEquals(expNbDistinctMatches, obsNbDistinctMatches)
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249 os.remove(tabFileName)
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250
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251 def test_convertMatchFileToAlignFile(self):
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252 inputMatchFileName = "file.tab"
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253 expAlignFileName = "expected.align"
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254 obsAlignFileName = "file.align"
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255
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256 self._writeExpAlignFile(expAlignFileName)
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257 self._writeMatchFile4(inputMatchFileName)
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258 MatchUtils.convertMatchFileToAlignFile(inputMatchFileName)
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259
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260 self.assertTrue(FileUtils.are2FilesIdentical(expAlignFileName, obsAlignFileName))
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261
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262 os.remove(inputMatchFileName)
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263 os.remove(expAlignFileName)
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264 os.remove(obsAlignFileName)
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265
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266 def test_convertMatchFileToAlignFile_empty_file(self):
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267 inputMatchFileName = "file.tab"
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268 expAlignFileName = "expected.align"
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269 obsAlignFileName = "file.align"
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270
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271 f = open(expAlignFileName, "w")
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272 f.close()
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273 f = open(inputMatchFileName, "w")
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274 f.close()
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275 MatchUtils.convertMatchFileToAlignFile(inputMatchFileName)
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276
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277 self.assertTrue(FileUtils.are2FilesIdentical(expAlignFileName, obsAlignFileName))
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278
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279 os.remove(inputMatchFileName)
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280 os.remove(expAlignFileName)
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281 os.remove(obsAlignFileName)
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282
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283 def test_generateMatchFileWithNewPathId(self):
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284 inputMatchFileName = "file.tab"
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285 expMatchFileName = "expected.tab"
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286 obsMatchFileName = "obsFile.tab"
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287
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288 self._writeMatchFile5(inputMatchFileName)
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289 self._writeExpMatchFile(expMatchFileName)
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290 MatchUtils.generateMatchFileWithNewPathId(inputMatchFileName, obsMatchFileName)
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291
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292 self.assertTrue(FileUtils.are2FilesIdentical(expMatchFileName, obsMatchFileName))
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293
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294 os.remove(inputMatchFileName)
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295 os.remove(expMatchFileName)
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296 os.remove(obsMatchFileName)
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297
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298 def test_generateMatchFileWithNewPathId_empty_file(self):
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299 inputMatchFileName = "file.tab"
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300 expMatchFileName = "expected.tab"
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301 obsMatchFileName = "obsFile.tab"
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302
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303 f = open(expMatchFileName, "w")
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304 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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305 f.close()
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306 f = open(inputMatchFileName, "w")
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307 f.close()
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308 MatchUtils.generateMatchFileWithNewPathId(inputMatchFileName, obsMatchFileName)
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309
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310 self.assertTrue(FileUtils.are2FilesIdentical(expMatchFileName, obsMatchFileName))
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311
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312 os.remove(inputMatchFileName)
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313 os.remove(expMatchFileName)
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314 os.remove(obsMatchFileName)
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315
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316 def test_convertMatchFileIntoABCFileOnQueryCoverage(self):
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317 matchFileName = "dummy.tab"
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318 with open(matchFileName, "w") as f:
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319 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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320 f.write("chr3\t1\t100\t100\t0.98\t0.95\tchr5\t11\t110\t100\t0.95\t1e-52\t133\t87.200000\n")
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321 f.write("chr7\t1\t200\t200\t0.98\t0.95\tchr2\t11\t210\t200\t0.95\t1e-78\t235\t98.900000\n")
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322 f.write("chr5\t1\t100\t100\t0.95\t0.95\tchr3\t11\t110\t100\t0.98\t1e-52\t133\t87.200000\n")
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323 f.write("chr2\t1\t200\t200\t0.95\t0.95\tchr7\t11\t210\t200\t0.98\t1e-78\t235\t98.900000\n")
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324 expFileName = "exp.abc"
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325 with open(expFileName, "w") as f:
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326 f.write("chr3\tchr5\t0.98\n")
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327 f.write("chr7\tchr2\t0.98\n")
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328 f.write("chr5\tchr3\t0.95\n")
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329 f.write("chr2\tchr7\t0.95\n")
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330 obsFileName = "obs.abc"
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331
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332 MatchUtils.convertMatchFileIntoABCFileOnQueryCoverage(matchFileName, obsFileName)
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333
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334 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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335
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336 os.remove(matchFileName)
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337 os.remove(expFileName)
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338 os.remove(obsFileName)
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339
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340 def test_convertMatchFileIntoABCFileOnQueryCoverage_coverage_threshold_85(self):
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341 matchFileName = "dummy.tab"
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342 with open(matchFileName, "w") as f:
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343 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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344 f.write("chr3\t1\t100\t100\t0.98\t0.95\tchr5\t11\t110\t100\t0.95\t1e-52\t133\t87.200000\n")
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345 f.write("chr7\t1\t200\t200\t0.98\t0.95\tchr2\t11\t210\t200\t0.95\t1e-78\t235\t98.900000\n")
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346 f.write("chr5\t1\t100\t100\t0.85\t0.95\tchr3\t11\t110\t100\t0.98\t1e-52\t133\t87.200000\n")
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347 f.write("chr2\t1\t200\t200\t0.80\t0.95\tchr7\t11\t210\t200\t0.98\t1e-78\t235\t98.900000\n")
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348 expFileName = "exp.abc"
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349 with open(expFileName, "w") as f:
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350 f.write("chr3\tchr5\t0.98\n")
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351 f.write("chr7\tchr2\t0.98\n")
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352 f.write("chr5\tchr3\t0.85\n")
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353 obsFileName = "obs.abc"
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354
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355 MatchUtils.convertMatchFileIntoABCFileOnQueryCoverage(matchFileName, obsFileName, coverage = 0.85)
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356
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357 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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358
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359 os.remove(matchFileName)
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360 os.remove(expFileName)
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361 os.remove(obsFileName)
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362
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363 def _writeFastaFile(self, fileName):
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364 f = open(fileName, "w")
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365 f.write(">HELITRON3\n")
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366 f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n")
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367 f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
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368 f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCTC\n")
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369 f.write(">HELITRON2\n")
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370 f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n")
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371 f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n")
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372 f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCTC\n")
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373 f.close()
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374
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375 def _writeMatchFile(self, fileName):
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376 f = open(fileName, "w")
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377 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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378 f.write("HELITRON3\t1\t180\t180\t1\t1\tHELITRON2\t1\t180\t180\t1\t2e-103\t357\t100\t1\n")
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379 f.close()
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380
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381 def _writeFastaFile2(self, fileName):
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382 f = open(fileName, "w")
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383 f.write(">header2\n")
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384 f.write("TTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGAATAAAAAATGATTATTTG\n")
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385 f.write("CATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGGGATTCGTTTCATTCACCG\n")
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386 f.close()
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387
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388 def _writeMatchFile2(self, fileName):
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389 f = open(fileName, "w")
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390 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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391 f.write("header2\t1\t120\t120\t1\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n")
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392 f.close()
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393
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394 def _writeMatchFile3(self, fileName):
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395 f = open(fileName, "w")
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396 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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397 f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n")
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398 f.write("header3\t1\t120\t120\t0.99\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-68\t238\t100\t1\n")
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399 f.write("header4\t1\t120\t120\t1\t0.94157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t67\t1\n")
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400 f.close()
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401
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402 def _writeMatchFile4(self, fileName):
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403 f = open(fileName, "w")
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404 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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405 f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n")
|
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406 f.write("header3\t120\t220\t120\t0.99\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-65\t238\t100\t1\n")
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407 f.write("header4\t1\t120\t120\t1\t0.94157\tBS31790\t19\t138\t120\t0.674157\t3e-67\t244\t90\t1\n")
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|
408 f.close()
|
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|
409
|
|
|
410 def _writeExpAlignFile(self,fileName):
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411 f = open(fileName, "w")
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412 f.write("header2\t1\t120\tBS31790\t19\t138\t3e-68\t238.0\t100.0\n")
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|
413 f.write("header3\t120\t220\tBS31790\t19\t138\t3e-65\t238.0\t100.0\n")
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414 f.write("header4\t1\t120\tBS31790\t19\t138\t3e-67\t244.0\t90.0\n")
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|
415 f.close()
|
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|
416
|
|
|
417 def _writeMatchFile5(self,fileName):
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|
418 f = open(fileName, "w")
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|
419 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
|
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|
420 f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n")
|
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421 f.write("header2\t124\t144\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n")
|
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|
422 f.write("header3\t120\t220\t120\t0.99\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-65\t238\t100\t1\n")
|
|
|
423 f.write("header4\t1\t120\t120\t1\t0.94157\tBS31790\t19\t138\t120\t0.674157\t3e-67\t244\t90\t1\n")
|
|
|
424 f.close()
|
|
|
425
|
|
|
426 def _writeExpMatchFile(self,fileName):
|
|
|
427 f = open(fileName, "w")
|
|
|
428 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
|
|
|
429 f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100.000000\t1\n")
|
|
|
430 f.write("header2\t124\t144\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100.000000\t1\n")
|
|
|
431 f.write("header3\t120\t220\t120\t0.990000\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-65\t238\t100.000000\t2\n")
|
|
|
432 f.write("header4\t1\t120\t120\t1.000000\t0.941570\tBS31790\t19\t138\t120\t0.674157\t3e-67\t244\t90.000000\t3\n")
|
|
|
433 f.close()
|
|
|
434
|
|
|
435
|
|
|
436 test_suite = unittest.TestSuite()
|
|
|
437 test_suite.addTest( unittest.makeSuite( Test_MatchUtils ) )
|
|
|
438 if __name__ == "__main__":
|
|
|
439 unittest.TextTestRunner(verbosity=2).run( test_suite )
|
