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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 from commons.core.coord.Range import Range
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34 from commons.core.coord.Range import getBin, getIdx
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35
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36
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37 class Test_Range( unittest.TestCase ):
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38
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39 def setUp(self):
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40 self._range = Range()
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41
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42 def test_setFromString(self):
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43 line = "chunk1\t190000\t390000"
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44 self._range.setFromString( line )
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45 self.assertEqual( self._range.seqname, "chunk1" )
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46 self.assertEqual( self._range.start, 190000 )
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47 self.assertEqual( self._range.end, 390000 )
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48
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49 line = "chunk1\t190000\t390000\n"
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50 self._range.setFromString( line )
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51 self.assertEqual( self._range.seqname, "chunk1" )
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52 self.assertEqual( self._range.start, 190000 )
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53 self.assertEqual( self._range.end, 390000 )
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54
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55 line = "chunk1;190000;390000"
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56 self._range.setFromString( line, ";" )
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57 self.assertEqual( self._range.seqname, "chunk1" )
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58 self.assertEqual( self._range.start, 190000 )
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59 self.assertEqual( self._range.end, 390000 )
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60
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61 def test_setFromTuple(self):
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62 tuple = ("chunk1","190000","390000")
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63 self._range.setFromTuple( tuple)
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64
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65 self.assertEqual( self._range.seqname, "chunk1" )
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66 self.assertEqual( self._range.start, 190000 )
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67 self.assertEqual( self._range.end, 390000 )
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68
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69 def test___eq__(self):
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70 self._range.setFromString( "chunk1\t190000\t390000\n" )
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71 o = Range()
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72 o.setFromString( "chunk1\t190000\t390000\n" )
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73 self.assertEqual( self._range, o )
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74
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75 o.setFromString( "chunk1\t190000\t39" )
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76 self.assertNotEquals( self._range, o )
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77
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78 o.setFromString( "chromosome1\t190000\t390000" )
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79 self.assertNotEquals( self._range, o )
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80
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81 o.setFromString( "chunk1\t390000\t190000" )
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82 self.assertNotEquals( self._range, o )
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83
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84 o.setFromString( "chromosome1\t390000\t190000" )
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85 self.assertNotEquals( self._range, o )
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86
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87 def test_getMin(self):
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88 self._range.setFromTuple( ("chunk1", 190000, 390000) )
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89 expMin = 190000
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90 obsMin = self._range.getMin()
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91 self.assertTrue(expMin, obsMin)
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92
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93 def test_getMax(self):
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94 self._range.setFromTuple( ("chunk1", 190000, 390000) )
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95 expMax = 390000
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96 obsMax = self._range.getMax()
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97 self.assertTrue(expMax, obsMax)
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98
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99 def test_isOnDirectStrand_true(self):
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100 self._range.setFromTuple( ("chunk1", 190000, 390000) )
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101 self.assertTrue(self._range.isOnDirectStrand())
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102
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103 def test_isOnDirectStrand_false(self):
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104 self._range.setFromTuple( ("chunk1", 390000, 190000) )
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105 self.assertFalse(self._range.isOnDirectStrand())
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106
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107 def test_isOnReverseStrand_true(self):
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108 self._range.setFromTuple( ("chunk1", 390000, 190000) )
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109 self.assertTrue(self._range.isOnReverseStrand())
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110
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111 def test_isOnReverseStrand_false(self):
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112 self._range.setFromTuple( ("chunk1", 190000, 390000) )
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113 self.assertFalse(self._range.isOnReverseStrand())
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114
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115 def test_getStrand_direct(self):
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116 self._range.setFromTuple( ("chunk1", 190000, 390000) )
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117 expStrand = '+'
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118 obsStrand = self._range.getStrand()
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119 self.assertEqual(expStrand, obsStrand)
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120
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121 def test_getStrand_reverse(self):
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122 self._range.setFromTuple( ("chunk1", 390000, 190000) )
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123 expStrand = '-'
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124 obsStrand = self._range.getStrand()
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125 self.assertEqual(expStrand, obsStrand)
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126
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127 def test_reverse(self):
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128 obsRange = Range("chunk1", 190000, 390000)
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129 expRange = Range("chunk1", 390000, 190000)
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130 obsRange.reverse()
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131 self.assertEquals(expRange, obsRange)
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132
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133 def test_getLength(self):
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134 self._range.setFromTuple( ("chunk1", 190000, 390000) )
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135 expLength = 200001
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136 obsLength = self._range.getLength()
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137 self.assertEquals(expLength, obsLength)
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138
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139 def test_isEmpty_true( self ):
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140 exp = True
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141 obs = self._range.isEmpty()
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142 self.assertEquals( exp, obs )
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143
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144 def test_isEmpty_false( self ):
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145 self._range.setFromTuple( ( "seq1", 1, 10 ) )
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146 exp = False
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147 obs = self._range.isEmpty()
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148 self.assertEquals( exp, obs )
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149
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150 def test_merge_diff_sequences( self ):
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151 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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152 range2 = Range( "seq2", 6, 12 )
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153 expReturn = None
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154 expRange = Range( "seq1", 6, 10 )
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155 obsReturn = self._range.merge( range2 )
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156 obsRange = self._range
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157 self.assertEquals( expReturn, obsReturn )
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158 self.assertEquals( expRange, obsRange )
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159
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160 def test_merge_no_overlapping_ranges( self ):
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161 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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162 range2 = Range( "seq1", 12, 20 )
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163 expReturn = None
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164 expRange = Range( "seq1", 6, 20 )
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165 obsReturn = self._range.merge( range2 )
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166 obsRange = self._range
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167 self.assertEquals( expReturn, obsReturn )
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168 self.assertEquals( expRange, obsRange )
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169
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170 def test_merge_no_overlapping_ranges_range1_on_neg_strand( self ):
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171 self._range.setFromTuple( ( "seq1", 10, 6 ) )
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172 range2 = Range( "seq1", 12, 20 )
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173 expReturn = None
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174 expRange = Range( "seq1", 20, 6 )
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175 obsReturn = self._range.merge( range2 )
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176 obsRange = self._range
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177 self.assertEquals( expReturn, obsReturn )
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178 self.assertEquals( expRange, obsRange )
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179
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180 def test_merge_overlapping_ranges_range1_and_range2_on_neg_strand( self ):
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181 self._range.setFromTuple( ( "seq1", 10, 6 ) )
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182 range2 = Range( "seq1", 20, 12 )
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183 expReturn = None
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184 expRange = Range( "seq1", 20, 6 )
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185 obsReturn = self._range.merge( range2 )
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186 obsRange = self._range
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187 self.assertEquals( expReturn, obsReturn )
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188 self.assertEquals( expRange, obsRange )
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189
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190 def test_merge_on_overlapping_ranges_range1_and_range2( self ):
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191 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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192 range2 = Range( "seq1", 8, 20 )
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193 expReturn = None
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194 expRange = Range( "seq1", 6, 20 )
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195 obsReturn = self._range.merge( range2 )
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196 obsRange = self._range
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197 self.assertEquals( expReturn, obsReturn )
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198 self.assertEquals( expRange, obsRange )
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199
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200 def test_isOverlapping_diff_sequences( self ):
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201 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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202 r2 = Range( "seq2", 6, 10 )
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203 exp = False
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204 obs = self._range.isOverlapping( r2 )
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205 self.assertEquals( exp, obs )
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206
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207 def test_isOverlapping_no( self ):
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208 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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209 r2 = Range( "seq1", 16, 20 )
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210 exp = False
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211 obs = self._range.isOverlapping( r2 )
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212 self.assertEquals( exp, obs )
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213
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214 def test_isOverlapping_yes( self ):
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215 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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216 r2 = Range( "seq1", 1, 15 )
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217 exp = True
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218 obs = self._range.isOverlapping( r2 )
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219 self.assertEquals( exp, obs )
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220
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221 def test_isOverlapping_yes_range2_on_neg_strand( self ):
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222 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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223 r2 = Range( "seq1", 15, 1 )
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224 exp = True
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225 obs = self._range.isOverlapping( r2 )
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226 self.assertEquals( exp, obs )
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227
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228 def test_isOverlapping_range1_before_range2( self ):
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229 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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230 r2 = Range( "seq1", 8, 15 )
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231 exp = True
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232 obs = self._range.isOverlapping( r2 )
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233 self.assertEquals( exp, obs )
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234
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235 def test_isOverlapping_range1_after_range2( self ):
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236 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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237 r2 = Range( "seq1", 1, 8 )
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238 exp = True
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239 obs = self._range.isOverlapping( r2 )
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240 self.assertEquals( exp, obs )
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241
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242 def test_isOverlapping_range1_equal_range2( self ):
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243 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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244 r2 = Range( "seq1", 6, 10 )
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245 exp = True
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246 obs = self._range.isOverlapping( r2 )
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247 self.assertEquals( exp, obs )
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248
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249 def test_isOverlapping_yes_edges_left( self ):
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250 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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251 r2 = Range( "seq1", 1, 6 )
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252 exp = True
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253 obs = self._range.isOverlapping( r2 )
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254 self.assertEquals( exp, obs )
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255
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256 def test_isOverlapping_yes_edges_right( self ):
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257 self._range.setFromTuple( ( "seq1", 6, 10 ) )
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258 r2 = Range( "seq1", 10, 20 )
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259 exp = True
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260 obs = self._range.isOverlapping( r2 )
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261 self.assertEquals( exp, obs )
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262
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263 def test_isOverlapping_yes_one_nt( self ):
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264 self._range.setFromTuple( ( "seq1", 10, 10 ) )
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265 r2 = Range( "seq1", 10, 20 )
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266 exp = True
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267 obs = self._range.isOverlapping( r2 )
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268 self.assertEquals( exp, obs )
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269
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270 def test_isOverlapping_yes_span_1( self ):
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271 self._range.setFromTuple( ( "seq1", 10, 100 ) )
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272 r2 = Range( "seq1", 5, 110 )
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273 exp = True
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274 obs = self._range.isOverlapping( r2 )
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275 self.assertEquals( exp, obs )
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276
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277 def test_isOverlapping_yes_span_2( self ):
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278 self._range.setFromTuple( ( "seq1", 5, 110 ) )
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279 r2 = Range( "seq1", 10, 100 )
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280 exp = True
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281 obs = self._range.isOverlapping( r2 )
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282 self.assertEquals( exp, obs )
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283
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284 def test_isOverlapping_yes_include_1( self ):
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285 self._range.setFromTuple( ( "seq1", 10, 100 ) )
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286 r2 = Range( "seq1", 15, 90 )
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287 exp = True
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288 obs = self._range.isOverlapping( r2 )
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289 self.assertEquals( exp, obs )
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290
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291 def test_isOverlapping_yes_include_2( self ):
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292 self._range.setFromTuple( ( "seq1", 15, 90 ) )
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293 r2 = Range( "seq1", 10, 100 )
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294 exp = True
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295 obs = self._range.isOverlapping( r2 )
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296 self.assertEquals( exp, obs )
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297
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298 def test_getOverlapLength_on_different_range( self ):
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299 range1 = Range( "chunk1", 190000, 390000 )
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300 range2 = Range( "chunk2", 290000, 590000 )
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301 expSize = 0
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302 obsSize = range1.getOverlapLength( range2 )
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303 self.assertEquals( expSize, obsSize )
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304
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305
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306 def test_getOverlapLength_on_no_overalping_range( self ):
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307 range1 =Range( "chunk1", 190000, 390000 )
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308 range2 =Range( "chunk1", 490000, 590000 )
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309 expSize = 0
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310 obsSize = range1.getOverlapLength( range2 )
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311 self.assertEquals( expSize, obsSize )
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312
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313
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314 def test_getOverlapLength_range2_included_in_range1( self ):
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315 range1 = Range( "chunk1", 19, 39 )
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316 range2 = Range( "chunk1", 22, 25 )
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317 expSize = 4
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318 obsSize = range1.getOverlapLength( range2 )
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319 self.assertEquals( expSize, obsSize )
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320 obsSize = range2.getOverlapLength( range1 )
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321 self.assertEquals( expSize, obsSize )
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322
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323
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324 def test_getOverlapLength_range1_included_in_range2( self ):
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325 range1 = Range( "chunk1", 220000, 250000 )
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326 range2 = Range( "chunk1", 190000, 390000 )
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327 expSize = 30001
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328 obsSize = range1.getOverlapLength( range2 )
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329 self.assertEquals( expSize, obsSize )
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330
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331
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332 def test_getOverlapLength_range1_before_range2( self ):
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333 range1 = Range( "chunk1", 190000, 390000 )
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334 range2 = Range( "chunk1", 290000, 590000 )
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335 expSize = 100001
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336 obsSize = range1.getOverlapLength( range2 )
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337 self.assertEquals( expSize, obsSize )
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338
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339
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340 def test_getOverlapLength_range1_after_range2( self ):
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341 range1 = Range( "chunk1", 390000, 790000 )
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342 range2 = Range( "chunk1", 290000, 590000 )
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343 expSize = 200001
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344 obsSize = range1.getOverlapLength( range2 )
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345 self.assertEquals( expSize, obsSize )
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346
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347
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348 def test_isIncludedIn( self ):
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349 iRange1 = Range( "chunk1", 21, 30 )
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350 iRange2 = Range( "chunk1", 11, 40 )
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351 self.assertTrue( iRange1.isIncludedIn( iRange2 ) )
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352
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353
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354 def test_isIncludedIn_diffStrand( self ):
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355 iRange1 = Range( "chunk1", 21, 30 )
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356 iRange2 = Range( "chunk1", 40, 11 )
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357 self.assertTrue( iRange1.isIncludedIn( iRange2 ) )
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358
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359
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360 def test_isIncludedIn_onlyOverlap( self ):
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361 iRange1 = Range( "chunk1", 21, 50 )
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362 iRange2 = Range( "chunk1", 11, 40 )
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363 self.assertFalse( iRange1.isIncludedIn( iRange2 ) )
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364
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365
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366 def test_isIncludedIn_diffSeqname( self ):
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367 iRange1 = Range( "chunk1", 21, 30 )
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368 iRange2 = Range( "chunk2", 11, 40 )
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369 self.assertFalse( iRange1.isIncludedIn( iRange2 ) )
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370
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371
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372 def test_getDistance_on_overlapping_range(self):
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373 overlapTuple1 = ("chunk1", 220000, 250000)
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374 overlapRange1 = Range()
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375 overlapRange1.setFromTuple(overlapTuple1)
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376
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377 overlapTuple2 = ("chunk1", 190000, 390000)
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378 overlapRange2 = Range()
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379 overlapRange2.setFromTuple(overlapTuple2)
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380
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381 expDistance = 0
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382 obsDistance = overlapRange1.getDistance(overlapRange2)
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383
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384 self.assertEquals(expDistance, obsDistance)
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385
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386 def test_getDistance_on_range1_on_plus_strand_included_in_range2_on_neg_strand(self):
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387 tuple1 = ("chunk1", 220000, 250000)
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388 range1 = Range()
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389 range1.setFromTuple(tuple1)
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390
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391 tuple2 = ("chunk1", 390000, 190000)
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392 range2 = Range()
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393 range1.setFromTuple(tuple2)
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394
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395 expDistance = -1
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396 obsDistance = range1.getDistance(range2)
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397
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398 self.assertEquals(expDistance, obsDistance)
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399
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400 def test_getDistance_range1_after_range2(self):
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401 tuple1 = ("chunk1", 390000, 590000)
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402 range1 = Range()
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403 range1.setFromTuple(tuple1)
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404
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405 tuple2 = ("chunk1", 190000, 290000)
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406 range2 = Range()
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407 range2.setFromTuple(tuple2)
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408
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409 expDistance = 100000
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410 obsDistance = range1.getDistance(range2)
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411
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412 self.assertEquals(expDistance, obsDistance)
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413
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414 def test_getDistance_range1_before_range2(self):
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415 tuple1 = ("chunk1", 190000, 290000)
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416 range1 = Range()
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417 range1.setFromTuple(tuple1)
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418
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419 tuple2 = ("chunk1", 390000, 590000)
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420 range2 = Range()
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421 range2.setFromTuple(tuple2)
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422
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423 expDistance = 100000
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424 obsDistance = range1.getDistance(range2)
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425
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426 self.assertEquals(expDistance, obsDistance)
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427
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428 def test_getDistance_range1_after_range2_both_on_neg_strand(self):
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429 tuple1 = ("chunk1", 590000, 390000)
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430 range1 = Range()
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431 range1.setFromTuple(tuple1)
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432
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433 tuple2 = ("chunk1", 290000, 190000)
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434 range2 = Range()
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435 range2.setFromTuple(tuple2)
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436
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437 expDistance = 100000
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438 obsDistance = range1.getDistance(range2)
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439
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440 self.assertEquals(expDistance, obsDistance)
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441
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442 def test_getDistance_range1_before_range2_both_on_neg_strand(self):
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443 tuple1 = ("chunk1", 290000, 190000)
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444 range1 = Range()
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445 range1.setFromTuple(tuple1)
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446
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447 tuple2 = ("chunk1", 590000, 390000)
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448 range2 = Range()
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449 range2.setFromTuple(tuple2)
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450
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451 expDistance = 100000
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452 obsDistance = range1.getDistance(range2)
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453
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454 self.assertEquals(expDistance, obsDistance)
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455
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456 def test_diff_on_no_overlapping_range(self):
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457 range1 = Range("chunk1", 190000, 390000)
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458 range2 = Range("chunk1", 490000, 590000)
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459
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460 expRange1 = Range("chunk1",190000,390000)
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461 expReturnedRange = Range("chunk1")
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462
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463 obsReturnedRange = range1.diff(range2)
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464 obsRange1 = range1
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465
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466 self.assertEquals(expRange1, obsRange1)
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467 self.assertEquals(expReturnedRange, obsReturnedRange)
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|
468
|
|
469 def test_diff_on_different_chunks(self):
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470 range1 = Range("chunk1", 190000, 390000)
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471 range2 = Range("chunk2", 290000, 590000)
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472
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473 expRange1 = Range("chunk1", 190000, 390000)
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474 expReturnedRange = Range("chunk1")
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475
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476 obsReturnedRange = range1.diff(range2)
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477 obsRange1 = range1
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478
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|
479 self.assertEquals(expRange1, obsRange1)
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480 self.assertEquals(expReturnedRange, obsReturnedRange)
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|
481
|
|
482 def test_diff_range1_before_range2(self):
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483 range1 = Range("chunk1", 190000, 390000)
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484 range2 = Range("chunk1", 290000, 590000)
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|
485
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486 expRange1 = Range("chunk1", 190000, 289999)
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487 expReturnedRange = Range("chunk1")
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|
488
|
|
489 obsReturnedRange = range1.diff(range2)
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490 obsRange1 = range1
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|
491
|
|
492 self.assertEquals(expRange1, obsRange1)
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|
493 self.assertEquals(expReturnedRange, obsReturnedRange)
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|
494
|
|
495 def test_diff_range1_before_range2_range1_on_neg_strand(self):
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496 range1 = Range("chunk1", 390000, 190000)
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497 range2 = Range("chunk1", 290000, 590000)
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|
498
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499 expRange1 = Range("chunk1", 289999, 190000)
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|
500 expReturnedRange = Range("chunk1")
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|
501
|
|
502 obsReturnedRange = range1.diff(range2)
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|
503 obsRange1 = range1
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|
504
|
|
505 self.assertEquals(expRange1, obsRange1)
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|
506 self.assertEquals(expReturnedRange, obsReturnedRange)
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|
507
|
|
508 def test_diff_range2_included_in_range1(self):
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|
509 range1 = Range("chunk1", 190000, 590000)
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|
510 range2 = Range("chunk1", 290000, 390000)
|
|
511
|
|
512 expRange1 = Range("chunk1", 190000, 289999)
|
|
513 expReturnedRange = Range("chunk1", 390001, 590000)
|
|
514
|
|
515 obsReturnedRange = range1.diff(range2)
|
|
516 obsRange1 = range1
|
|
517
|
|
518 self.assertEquals(expRange1, obsRange1)
|
|
519 self.assertEquals(expReturnedRange, obsReturnedRange)
|
|
520
|
|
521 def test_diff_range2_included_in_range1_range1_on_reverse_strand(self):
|
|
522 range1 = Range("chunk1", 590000, 190000)
|
|
523 range2 = Range("chunk1", 290000, 390000)
|
|
524
|
|
525 expRange1 = Range("chunk1", 289999, 190000)
|
|
526 expReturnedRange = Range("chunk1", 590000, 390001)
|
|
527
|
|
528 obsReturnedRange = range1.diff(range2)
|
|
529 obsRange1 = range1
|
|
530
|
|
531 self.assertEquals(expRange1, obsRange1)
|
|
532 self.assertEquals(expReturnedRange, obsReturnedRange)
|
|
533
|
|
534 def test_diff_range1_included_in_range2(self):
|
|
535 range1 = Range("chunk1", 390000, 490000)
|
|
536 range2 = Range("chunk1", 290000, 590000)
|
|
537
|
|
538 expRange1 = Range("chunk1",0,0)
|
|
539 expReturnedRange = Range("chunk1")
|
|
540
|
|
541 obsReturnedRange = range1.diff(range2)
|
|
542 obsRange1 = range1
|
|
543
|
|
544 self.assertEquals(expRange1, obsRange1)
|
|
545 self.assertEquals(expReturnedRange, obsReturnedRange)
|
|
546
|
|
547 def test_diff_range1_after_range2(self):
|
|
548 range1 = Range("chunk1", 390000, 590000)
|
|
549 range2 = Range("chunk1", 290000, 490000)
|
|
550
|
|
551 expRange1 = Range("chunk1", 490001, 590000)
|
|
552 expReturnedRange = Range("chunk1")
|
|
553
|
|
554 obsReturnedRange = range1.diff(range2)
|
|
555 obsRange1 = range1
|
|
556
|
|
557 self.assertEquals(expRange1, obsRange1)
|
|
558 self.assertEquals(expReturnedRange, obsReturnedRange)
|
|
559
|
|
560 def test_diff_range1_after_range2_range1_on_neg_strand(self):
|
|
561 range1 = Range("chunk1", 590000, 390000)
|
|
562 range2 = Range("chunk1", 290000, 490000)
|
|
563
|
|
564 expRange1 = Range("chunk1", 590000, 490001)
|
|
565 expReturnedRange = Range("chunk1")
|
|
566
|
|
567 obsReturnedRange = range1.diff(range2)
|
|
568 obsRange1 = range1
|
|
569
|
|
570 self.assertEquals(expRange1, obsRange1)
|
|
571 self.assertEquals(expReturnedRange, obsReturnedRange)
|
|
572
|
|
573 def test_getIdx(self):
|
|
574 self.assertEqual(getIdx(1000,3),1000001)
|
|
575 self.assertEqual(getIdx(999,3),1000000)
|
|
576 self.assertEqual(getIdx(2000,3),1000002)
|
|
577 self.assertEqual(getIdx(2000,4),2000000)
|
|
578 self.assertEqual(getIdx(2000,5),3000000)
|
|
579 self.assertEqual(getIdx(20000000,6),4000000)
|
|
580 self.assertEqual(getIdx(20000000,5),3000200)
|
|
581 self.assertEqual(getIdx(20000000,4),2002000)
|
|
582 self.assertEqual(getIdx(20000000,3),1020000)
|
|
583
|
|
584 def test_getBin_bin_level_9(self):
|
|
585 tuple1 = ("chunk1", 190000000, 390000000)
|
|
586 range1 =Range()
|
|
587 range1.setFromTuple(tuple1)
|
|
588
|
|
589 expRes = 100000000.0
|
|
590 obsRes = range1.getBin()
|
|
591
|
|
592 self.assertEquals(expRes, obsRes)
|
|
593
|
|
594 def test_getBin_bin_level_8(self):
|
|
595 tuple1 = ("chunk1", 19000000, 39000000)
|
|
596 range1 =Range()
|
|
597 range1.setFromTuple(tuple1)
|
|
598
|
|
599 expRes = 100000000.0
|
|
600 obsRes = range1.getBin()
|
|
601
|
|
602 self.assertEquals(expRes, obsRes)
|
|
603
|
|
604 def test_getBin_bin_level_7(self):
|
|
605 tuple1 = ("chunk1", 1900000, 3900000)
|
|
606 range1 =Range()
|
|
607 range1.setFromTuple(tuple1)
|
|
608
|
|
609 expRes = 10000000.0
|
|
610 obsRes = range1.getBin()
|
|
611
|
|
612 self.assertEquals(expRes, obsRes)
|
|
613
|
|
614 def test_getBin_bin_level_6(self):
|
|
615 tuple1 = ("chunk1", 190000, 390000)
|
|
616 range1 =Range()
|
|
617 range1.setFromTuple(tuple1)
|
|
618
|
|
619 expRes = 1000000.0
|
|
620 obsRes = range1.getBin()
|
|
621
|
|
622 self.assertEquals(expRes, obsRes)
|
|
623
|
|
624 def test_getBin_bin_level_5(self):
|
|
625 tuple = ("chunk1", 19000, 39000)
|
|
626 range =Range()
|
|
627 range.setFromTuple(tuple)
|
|
628 expRes = 100000.0
|
|
629 obsRes = range.getBin()
|
|
630
|
|
631 self.assertEquals(expRes, obsRes)
|
|
632
|
|
633 def test_getBin_bin_level_4(self):
|
|
634 tuple = ("chunk1", 1900, 3900)
|
|
635 range =Range()
|
|
636 range.setFromTuple(tuple)
|
|
637
|
|
638 expRes = 10000.0
|
|
639 obsRes = range.getBin()
|
|
640
|
|
641 self.assertEquals(expRes, obsRes)
|
|
642
|
|
643 def test_getBin_bin_level_3(self):
|
|
644 tuple = ("chunk1", 190, 390)
|
|
645 range =Range()
|
|
646 range.setFromTuple(tuple)
|
|
647
|
|
648 expRes = 1000.0
|
|
649 obsRes = range.getBin()
|
|
650
|
|
651 self.assertEquals(expRes, obsRes)
|
|
652
|
|
653 def test_getBin_bin_level_2(self):
|
|
654 tuple = ("chunk1", 19, 39)
|
|
655 range =Range()
|
|
656 range.setFromTuple(tuple)
|
|
657
|
|
658 expRes = 1000.0
|
|
659 obsRes = range.getBin()
|
|
660
|
|
661 self.assertEquals(expRes, obsRes)
|
|
662
|
|
663 def test_getBin_bin_level_1(self):
|
|
664 tuple = ("chunk1", 1, 3)
|
|
665 range =Range()
|
|
666 range.setFromTuple(tuple)
|
|
667
|
|
668 expRes = 1000.0
|
|
669 obsRes = range.getBin()
|
|
670
|
|
671 self.assertEquals(expRes, obsRes)
|
|
672
|
|
673
|
|
674 def test_getBin_function(self):
|
|
675 expBin = 2L
|
|
676 obsBin = getBin(200, 2)
|
|
677
|
|
678 self.assertEquals(expBin, obsBin)
|
|
679
|
|
680 def test_findIdx(self):
|
|
681 o = Range()
|
|
682 o.setFromString( "chunk1\t1000\t2000\n" )
|
|
683 self.assertEqual(o.findIdx(),2000000)
|
|
684
|
|
685 o.setFromString( "chunk1\t2000\t1000\n" )
|
|
686 self.assertEqual(o.findIdx(),2000000)
|
|
687
|
|
688 o.setFromString( "chunk1\t200\t999\n" )
|
|
689 self.assertEqual(o.findIdx(),1000000)
|
|
690
|
|
691 o.setFromString( "chunk1\t1\t20000000\n" )
|
|
692 self.assertEqual(o.findIdx(),4000000)
|
|
693
|
|
694
|
|
695 test_suite = unittest.TestSuite()
|
|
696 test_suite.addTest( unittest.makeSuite( Test_Range ) )
|
|
697 if __name__ == "__main__":
|
|
698 unittest.TextTestRunner(verbosity=2).run( test_suite )
|