Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/coord/test/Test_Range.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 |
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271 def test_getOverlapLength_on_different_range( self ): |
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272 range1 = Range( "chunk1", 190000, 390000 ) |
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273 range2 = Range( "chunk2", 290000, 590000 ) |
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274 expSize = 0 |
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275 obsSize = range1.getOverlapLength( range2 ) |
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276 self.assertEquals( expSize, obsSize ) |
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277 |
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278 |
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279 def test_getOverlapLength_on_no_overalping_range( self ): |
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280 range1 =Range( "chunk1", 190000, 390000 ) |
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281 range2 =Range( "chunk1", 490000, 590000 ) |
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282 expSize = 0 |
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283 obsSize = range1.getOverlapLength( range2 ) |
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284 self.assertEquals( expSize, obsSize ) |
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285 |
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286 |
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287 def test_getOverlapLength_range2_included_in_range1( self ): |
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288 range1 = Range( "chunk1", 19, 39 ) |
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289 range2 = Range( "chunk1", 22, 25 ) |
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290 expSize = 4 |
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291 obsSize = range1.getOverlapLength( range2 ) |
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292 self.assertEquals( expSize, obsSize ) |
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293 obsSize = range2.getOverlapLength( range1 ) |
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294 self.assertEquals( expSize, obsSize ) |
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295 |
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296 |
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297 def test_getOverlapLength_range1_included_in_range2( self ): |
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298 range1 = Range( "chunk1", 220000, 250000 ) |
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299 range2 = Range( "chunk1", 190000, 390000 ) |
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300 expSize = 30001 |
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301 obsSize = range1.getOverlapLength( range2 ) |
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302 self.assertEquals( expSize, obsSize ) |
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303 |
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304 |
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305 def test_getOverlapLength_range1_before_range2( self ): |
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306 range1 = Range( "chunk1", 190000, 390000 ) |
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307 range2 = Range( "chunk1", 290000, 590000 ) |
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308 expSize = 100001 |
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309 obsSize = range1.getOverlapLength( range2 ) |
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310 self.assertEquals( expSize, obsSize ) |
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311 |
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312 |
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313 def test_getOverlapLength_range1_after_range2( self ): |
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314 range1 = Range( "chunk1", 390000, 790000 ) |
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315 range2 = Range( "chunk1", 290000, 590000 ) |
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316 expSize = 200001 |
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317 obsSize = range1.getOverlapLength( range2 ) |
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318 self.assertEquals( expSize, obsSize ) |
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319 |
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320 |
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321 def test_isIncludedIn( self ): |
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322 iRange1 = Range( "chunk1", 21, 30 ) |
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323 iRange2 = Range( "chunk1", 11, 40 ) |
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324 self.assertTrue( iRange1.isIncludedIn( iRange2 ) ) |
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325 |
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326 |
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327 def test_isIncludedIn_diffStrand( self ): |
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328 iRange1 = Range( "chunk1", 21, 30 ) |
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329 iRange2 = Range( "chunk1", 40, 11 ) |
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330 self.assertTrue( iRange1.isIncludedIn( iRange2 ) ) |
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331 |
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332 |
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333 def test_isIncludedIn_onlyOverlap( self ): |
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334 iRange1 = Range( "chunk1", 21, 50 ) |
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335 iRange2 = Range( "chunk1", 11, 40 ) |
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336 self.assertFalse( iRange1.isIncludedIn( iRange2 ) ) |
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337 |
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338 |
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339 def test_isIncludedIn_diffSeqname( self ): |
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340 iRange1 = Range( "chunk1", 21, 30 ) |
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341 iRange2 = Range( "chunk2", 11, 40 ) |
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342 self.assertFalse( iRange1.isIncludedIn( iRange2 ) ) |
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343 |
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344 |
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345 def test_getDistance_on_overlapping_range(self): |
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346 overlapTuple1 = ("chunk1", 220000, 250000) |
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347 overlapRange1 = Range() |
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348 overlapRange1.setFromTuple(overlapTuple1) |
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349 |
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350 overlapTuple2 = ("chunk1", 190000, 390000) |
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351 overlapRange2 = Range() |
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352 overlapRange2.setFromTuple(overlapTuple2) |
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353 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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354 expDistance = 0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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355 obsDistance = overlapRange1.getDistance(overlapRange2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
356 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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357 self.assertEquals(expDistance, obsDistance) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
358 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
359 def test_getDistance_on_range1_on_plus_strand_included_in_range2_on_neg_strand(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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360 tuple1 = ("chunk1", 220000, 250000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
361 range1 = Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
362 range1.setFromTuple(tuple1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
363 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
364 tuple2 = ("chunk1", 390000, 190000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
365 range2 = Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
366 range1.setFromTuple(tuple2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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367 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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368 expDistance = -1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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369 obsDistance = range1.getDistance(range2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
370 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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371 self.assertEquals(expDistance, obsDistance) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
372 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
373 def test_getDistance_range1_after_range2(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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374 tuple1 = ("chunk1", 390000, 590000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
375 range1 = Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
376 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
377 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
378 tuple2 = ("chunk1", 190000, 290000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
379 range2 = Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
380 range2.setFromTuple(tuple2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
381 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
382 expDistance = 100000 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
383 obsDistance = range1.getDistance(range2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
384 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
385 self.assertEquals(expDistance, obsDistance) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
386 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
387 def test_getDistance_range1_before_range2(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
388 tuple1 = ("chunk1", 190000, 290000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
389 range1 = Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
390 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
391 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
392 tuple2 = ("chunk1", 390000, 590000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
393 range2 = Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
394 range2.setFromTuple(tuple2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
395 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
396 expDistance = 100000 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
397 obsDistance = range1.getDistance(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
398 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
399 self.assertEquals(expDistance, obsDistance) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
400 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
401 def test_getDistance_range1_after_range2_both_on_neg_strand(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
402 tuple1 = ("chunk1", 590000, 390000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
403 range1 = Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
404 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
405 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
406 tuple2 = ("chunk1", 290000, 190000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
407 range2 = Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
408 range2.setFromTuple(tuple2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
409 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
410 expDistance = 100000 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
411 obsDistance = range1.getDistance(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
412 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
413 self.assertEquals(expDistance, obsDistance) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
414 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
415 def test_getDistance_range1_before_range2_both_on_neg_strand(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
416 tuple1 = ("chunk1", 290000, 190000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
417 range1 = Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
418 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
419 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
420 tuple2 = ("chunk1", 590000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
421 range2 = Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
422 range2.setFromTuple(tuple2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
423 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
424 expDistance = 100000 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
425 obsDistance = range1.getDistance(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
426 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
427 self.assertEquals(expDistance, obsDistance) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
428 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
429 def test_diff_on_no_overlapping_range(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
430 range1 = Range("chunk1", 190000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
431 range2 = Range("chunk1", 490000, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
432 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
433 expRange1 = Range("chunk1",190000,390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
434 expReturnedRange = Range("chunk1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
435 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
436 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
437 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
438 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
439 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
440 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
441 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
442 def test_diff_on_different_chunks(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
443 range1 = Range("chunk1", 190000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
444 range2 = Range("chunk2", 290000, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
445 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
446 expRange1 = Range("chunk1", 190000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
447 expReturnedRange = Range("chunk1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
448 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
449 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
450 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
451 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
452 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
453 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
454 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
455 def test_diff_range1_before_range2(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
456 range1 = Range("chunk1", 190000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
457 range2 = Range("chunk1", 290000, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
458 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
459 expRange1 = Range("chunk1", 190000, 289999) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
460 expReturnedRange = Range("chunk1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
461 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
462 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
463 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
464 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
465 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
466 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
467 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
468 def test_diff_range1_before_range2_range1_on_neg_strand(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
469 range1 = Range("chunk1", 390000, 190000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
470 range2 = Range("chunk1", 290000, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
471 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
472 expRange1 = Range("chunk1", 289999, 190000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
473 expReturnedRange = Range("chunk1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
474 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
475 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
476 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
477 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
478 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
479 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
480 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
481 def test_diff_range2_included_in_range1(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
482 range1 = Range("chunk1", 190000, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
483 range2 = Range("chunk1", 290000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
484 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
485 expRange1 = Range("chunk1", 190000, 289999) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
486 expReturnedRange = Range("chunk1", 390001, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
487 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
488 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
489 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
490 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
491 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
492 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
493 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
494 def test_diff_range2_included_in_range1_range1_on_reverse_strand(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
495 range1 = Range("chunk1", 590000, 190000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
496 range2 = Range("chunk1", 290000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
497 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
498 expRange1 = Range("chunk1", 289999, 190000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
499 expReturnedRange = Range("chunk1", 590000, 390001) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
500 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
501 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
502 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
503 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
504 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
505 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
506 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
507 def test_diff_range1_included_in_range2(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
508 range1 = Range("chunk1", 390000, 490000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
509 range2 = Range("chunk1", 290000, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
510 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
511 expRange1 = Range("chunk1",0,0) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
512 expReturnedRange = Range("chunk1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
513 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
514 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
515 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
516 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
517 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
518 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
519 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
520 def test_diff_range1_after_range2(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
521 range1 = Range("chunk1", 390000, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
522 range2 = Range("chunk1", 290000, 490000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
523 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
524 expRange1 = Range("chunk1", 490001, 590000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
525 expReturnedRange = Range("chunk1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
526 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
527 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
528 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
529 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
530 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
531 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
532 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
533 def test_diff_range1_after_range2_range1_on_neg_strand(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
534 range1 = Range("chunk1", 590000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
535 range2 = Range("chunk1", 290000, 490000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
536 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
537 expRange1 = Range("chunk1", 590000, 490001) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
538 expReturnedRange = Range("chunk1") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
539 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
540 obsReturnedRange = range1.diff(range2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
541 obsRange1 = range1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
542 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
543 self.assertEquals(expRange1, obsRange1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
544 self.assertEquals(expReturnedRange, obsReturnedRange) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
545 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
546 def test_getIdx(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
547 self.assertEqual(getIdx(1000,3),1000001) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
548 self.assertEqual(getIdx(999,3),1000000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
549 self.assertEqual(getIdx(2000,3),1000002) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
550 self.assertEqual(getIdx(2000,4),2000000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
551 self.assertEqual(getIdx(2000,5),3000000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
552 self.assertEqual(getIdx(20000000,6),4000000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
553 self.assertEqual(getIdx(20000000,5),3000200) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
554 self.assertEqual(getIdx(20000000,4),2002000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
555 self.assertEqual(getIdx(20000000,3),1020000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
556 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
557 def test_getBin_bin_level_9(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
558 tuple1 = ("chunk1", 190000000, 390000000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
559 range1 =Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
560 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
562 expRes = 100000000.0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
563 obsRes = range1.getBin() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
564 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
565 self.assertEquals(expRes, obsRes) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
566 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
567 def test_getBin_bin_level_8(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
568 tuple1 = ("chunk1", 19000000, 39000000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 range1 =Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
570 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
571 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
572 expRes = 100000000.0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
573 obsRes = range1.getBin() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
574 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 self.assertEquals(expRes, obsRes) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
576 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 def test_getBin_bin_level_7(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
578 tuple1 = ("chunk1", 1900000, 3900000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
579 range1 =Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
580 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
581 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 expRes = 10000000.0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 obsRes = range1.getBin() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
584 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
585 self.assertEquals(expRes, obsRes) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
586 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
587 def test_getBin_bin_level_6(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 tuple1 = ("chunk1", 190000, 390000) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 range1 =Range() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 range1.setFromTuple(tuple1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
592 expRes = 1000000.0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 obsRes = range1.getBin() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 self.assertEquals(expRes, obsRes) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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596 |
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597 def test_getBin_bin_level_5(self): |
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598 tuple = ("chunk1", 19000, 39000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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599 range =Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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600 range.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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601 expRes = 100000.0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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602 obsRes = range.getBin() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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603 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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604 self.assertEquals(expRes, obsRes) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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605 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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606 def test_getBin_bin_level_4(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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607 tuple = ("chunk1", 1900, 3900) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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608 range =Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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609 range.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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610 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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611 expRes = 10000.0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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612 obsRes = range.getBin() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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613 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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614 self.assertEquals(expRes, obsRes) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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615 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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616 def test_getBin_bin_level_3(self): |
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617 tuple = ("chunk1", 190, 390) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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618 range =Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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619 range.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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620 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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621 expRes = 1000.0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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622 obsRes = range.getBin() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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623 |
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624 self.assertEquals(expRes, obsRes) |
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625 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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626 def test_getBin_bin_level_2(self): |
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627 tuple = ("chunk1", 19, 39) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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628 range =Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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629 range.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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630 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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631 expRes = 1000.0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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632 obsRes = range.getBin() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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633 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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634 self.assertEquals(expRes, obsRes) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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635 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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636 def test_getBin_bin_level_1(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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637 tuple = ("chunk1", 1, 3) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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638 range =Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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639 range.setFromTuple(tuple) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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640 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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641 expRes = 1000.0 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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642 obsRes = range.getBin() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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643 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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644 self.assertEquals(expRes, obsRes) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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645 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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646 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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647 def test_getBin_function(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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648 expBin = 2L |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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649 obsBin = getBin(200, 2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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650 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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651 self.assertEquals(expBin, obsBin) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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652 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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653 def test_findIdx(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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654 o = Range() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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655 o.setFromString( "chunk1\t1000\t2000\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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656 self.assertEqual(o.findIdx(),2000000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
657 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff
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658 o.setFromString( "chunk1\t2000\t1000\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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659 self.assertEqual(o.findIdx(),2000000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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660 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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661 o.setFromString( "chunk1\t200\t999\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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662 self.assertEqual(o.findIdx(),1000000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
663 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
664 o.setFromString( "chunk1\t1\t20000000\n" ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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665 self.assertEqual(o.findIdx(),4000000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
666 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
667 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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668 test_suite = unittest.TestSuite() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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669 test_suite.addTest( unittest.makeSuite( Test_Range ) ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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670 if __name__ == "__main__": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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671 unittest.TextTestRunner(verbosity=2).run( test_suite ) |