Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/coord/test/Test_Set.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 import os |
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34 from commons.core.coord.Set import Set |
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35 from commons.core.coord.Map import Map |
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36 |
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37 |
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38 class Test_Set( unittest.TestCase ): |
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39 |
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40 def test__eq__sets_equals(self): |
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41 set1 = Set( 1, "set1", "seq1", 1, 2 ) |
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42 set2 = Set( 1, "set1", "seq1", 1 ,2 ) |
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43 self.assertEquals( set1, set2 ) |
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44 |
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45 def test__eq__sets_not_equals_ids(self): |
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46 set1 = Set( 1, "set1", "seq1", 1, 2 ) |
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47 set2 = Set( 2, "set1", "seq1", 1 ,2 ) |
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48 self.assertNotEquals( set1, set2 ) |
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49 |
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50 def test__eq__sets_not_equals_name(self): |
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51 set1 = Set( 1, "set1", "seq1", 1, 2 ) |
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52 set2 = Set( 1, "set2", "seq1", 1 ,2 ) |
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53 self.assertNotEquals( set1, set2 ) |
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54 |
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55 def test__eq__on_empty_set(self): |
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56 set1 = Set() |
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57 set2 = Set() |
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58 self.assertEquals( set1, set2 ) |
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59 |
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60 def test_setFromTuple_equals_instances(self): |
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61 tuple = ( 1, "set1", "seq1", 1, 2 ) |
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62 obsSet = Set() |
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63 obsSet.setFromTuple(tuple) |
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64 expSet = Set( 1, "set1", "seq1", 1, 2 ) |
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65 self.assertEquals( expSet, obsSet ) |
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66 |
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67 def test_setFromTuple_not_equals_instances(self): |
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68 tuple = ( 1, "set1", "seq1", 1, 2 ) |
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69 obsSet = Set() |
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70 obsSet.setFromTuple(tuple) |
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71 expSet = Set( 2, "set1", "seq1", 1, 2 ) |
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72 self.assertNotEquals( expSet, obsSet ) |
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73 |
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74 def test_read_empty_line_file(self): |
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75 fileName = "dummyFile" |
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76 |
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77 os.system(" touch " + fileName) |
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78 |
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79 fileHandler = open(fileName, "r") |
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80 |
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81 obsSet = Set() |
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82 |
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83 obsRes = obsSet.read( fileHandler ) |
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84 expRes = 0 |
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85 |
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86 fileHandler.close() |
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87 os.remove(fileName) |
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88 |
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89 self.assertEquals( expRes, obsRes ) |
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90 |
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91 def test_read_one_line_file(self): |
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92 line = ( "1\tset1\tseq1\t1\t2" ) |
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93 fileName = "dummyFile" |
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94 |
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95 fileHandler = open( fileName, "w" ) |
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96 fileHandler.write( line ) |
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97 fileHandler.close() |
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98 |
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99 fileHandler = open( fileName, "r" ) |
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100 |
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101 tuple = line.split("\t") |
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102 expSet = Set() |
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103 expSet.setFromTuple(tuple) |
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104 |
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105 obsSet = Set() |
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106 |
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107 expRes = 1 |
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108 obsRes = obsSet.read(fileHandler) |
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109 |
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110 fileHandler.close() |
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111 os.remove(fileName) |
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112 self.assertEquals( expRes, obsRes ) |
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113 self.assertEquals( expSet, obsSet ) |
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114 |
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115 def test_read_two_line_file(self): |
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116 line1 = ( "1\tset1\tseq1\t1\t2\n" ) |
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117 line2 = ( "2\tset2\tseq2\t3\t4" ) |
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118 fileName = "dummyFile" |
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119 |
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120 fileHandler = open( fileName, "w" ) |
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121 fileHandler.write( line1 ) |
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122 fileHandler.write( line2 ) |
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123 fileHandler.close() |
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124 |
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125 tuple1 = line1.split("\t") |
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126 tuple2 = line2.split("\t") |
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127 |
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128 expSet1 = Set() |
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129 expSet2 = Set() |
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130 |
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131 expSet1.setFromTuple(tuple1) |
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132 expSet2.setFromTuple(tuple2) |
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133 |
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134 expSetList = [ expSet1, expSet2 ] |
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135 expResList = [ 1, 1 ] |
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136 |
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137 fileHandler = open( fileName, "r" ) |
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138 |
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139 obsSet1 = Set() |
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140 obsSet2 = Set() |
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141 |
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142 obsRes1 = obsSet1.read(fileHandler) |
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143 obsRes2 = obsSet2.read(fileHandler) |
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144 |
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145 obsSetList= [ obsSet1, obsSet2 ] |
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146 obsResList = [ obsRes1, obsRes2 ] |
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147 |
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148 fileHandler.close() |
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149 os.remove(fileName) |
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150 |
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151 self.assertEquals( expSetList, obsSetList ) |
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152 self.assertEquals( expResList, obsResList ) |
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153 |
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154 def test_merge_first_id_greater_than_second_id(self): |
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155 firstSet = Set( 2, "set1", "seq1", 10, 40 ) |
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156 secondSet = Set( 1, "set2", "seq1", 20, 60 ) |
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157 |
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158 firstSet.merge( secondSet ) |
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159 |
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160 expSet = Set( 1, "set1", "seq1", 10, 60) |
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161 obsSet = firstSet |
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162 |
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163 self.assertEquals( expSet, obsSet) |
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164 |
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165 def test_merge_first_id_smaller_than_second_id(self): |
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166 firstSet = Set( 1, "set1", "seq1", 10, 40 ) |
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167 secondSet = Set( 2, "set2", "seq1", 20, 60 ) |
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168 |
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169 firstSet.merge( secondSet ) |
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170 |
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171 expSet = Set( 1, "set1", "seq1", 10, 60) |
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172 obsSet = firstSet |
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173 |
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174 self.assertEquals( expSet, obsSet) |
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175 |
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176 def test_merge_first_id_equals_second_id(self): |
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177 firstSet = Set( 1, "set1", "seq1", 10, 40 ) |
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178 secondSet = Set( 1, "set2", "seq1", 20, 60 ) |
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179 |
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180 firstSet.merge( secondSet ) |
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181 |
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182 expSet = Set( 1, "set1", "seq1", 10, 60) |
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183 obsSet = firstSet |
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184 |
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185 self.assertEquals( expSet, obsSet) |
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186 |
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187 def test_merge_different_seqnames(self): |
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188 firstSet = Set( 2, "set1", "seq1", 10, 40 ) |
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189 secondSet = Set( 1, "set1", "seq2", 20, 60 ) |
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190 expSet = Set( 2, "set1", "seq1", 10, 40 ) |
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191 firstSet.merge( secondSet ) |
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192 obsSet = firstSet |
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193 self.assertEquals( expSet, obsSet ) |
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194 |
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195 def test_diff_on_empty_sets(self): |
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196 firstSet = Set() |
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197 firstSet.seqname = "seq1" |
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198 secondSet = Set() |
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199 secondSet.seqname = "seq2" |
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200 |
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201 obsSet = firstSet.diff( secondSet ) |
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202 expSet = Set() |
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203 |
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204 self.assertEquals( expSet, obsSet ) |
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205 |
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206 def test_diff(self): |
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207 firstSet = Set( 2, "set1", "seq1", 10, 80 ) |
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208 secondSet = Set( 1, "set2", "seq1", 20, 60 ) |
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209 |
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210 expSet1 = Set( 2, "set1", "seq1", 10, 19 ) |
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211 expSet2 = Set( 2, "set1", "seq1", 61, 80 ) |
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212 |
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213 obsSet2 = firstSet.diff( secondSet ) |
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214 obsSet1 = firstSet |
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215 |
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216 self.assertEquals( expSet1, obsSet1 ) |
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217 self.assertEquals( expSet2, obsSet2 ) |
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218 |
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219 def test_diff_reverse(self): |
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220 firstSet = Set( 2, "set1", "seq1", 20, 60 ) |
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221 secondSet = Set( 1, "set2", "seq1", 10, 80 ) |
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222 |
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223 expSet1 = Set( 2, "set1", "seq1", 0, 0 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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224 expSet2 = Set( ) |
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225 |
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226 obsSet2 = firstSet.diff( secondSet ) |
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227 obsSet1 = firstSet |
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228 |
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229 self.assertEquals( expSet1, obsSet1 ) |
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230 self.assertEquals( expSet2, obsSet2 ) |
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231 |
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232 def test_diff_list1_overlap_end_list2(self): |
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233 firstSet = Set( 2, "set1", "seq1", 20, 100 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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234 secondSet = Set( 1, "set2", "seq1", 10, 80 ) |
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235 |
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236 expSet1 = Set( 2, "set1", "seq1", 81, 100 ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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237 expSet2 = Set( ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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238 |
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239 obsSet2 = firstSet.diff( secondSet ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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240 obsSet1 = firstSet |
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241 |
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242 self.assertEquals( expSet1, obsSet1 ) |
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243 self.assertEquals( expSet2, obsSet2 ) |
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244 |
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245 def test_diff_with_empty_set1(self): |
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246 set2 = Set( 1, "set1", "seq1", 2, 45 ) |
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247 set1 = Set( ) |
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248 |
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249 expSet1 = Set( ) |
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250 expSet2 = Set( ) |
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251 |
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252 obsSet2 = set1.diff( set2 ) |
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253 obsSet1 = set1 |
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254 |
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255 self.assertEquals( expSet1, obsSet1 ) |
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256 self.assertEquals( expSet2, obsSet2 ) |
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257 |
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258 def test_diff_list2_overlap_end_list1(self): |
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259 firstSet = Set( 2, "set1", "seq1", 10, 70 ) |
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260 secondSet = Set( 1, "set2", "seq1", 40, 100 ) |
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261 |
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262 expSet1 = Set( 2, "set1", "seq1", 10, 39 ) |
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263 expSet2 = Set( ) |
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264 |
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265 obsSet2 = firstSet.diff( secondSet ) |
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266 obsSet1 = firstSet |
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267 |
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268 self.assertEquals( expSet1, obsSet1 ) |
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269 self.assertEquals( expSet2, obsSet2 ) |
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270 |
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271 def test_set2map(self): |
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272 set = Set( 1, "set", "seq", 1, 2 ) |
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273 |
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274 expMap = Map( "set::1", "seq", 1, 2 ) |
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275 obsMap = set.set2map() |
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276 |
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277 self.assertEquals( expMap, obsMap ) |
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278 |
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279 test_suite = unittest.TestSuite() |
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280 test_suite.addTest( unittest.makeSuite( Test_Set ) ) |
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281 if __name__ == "__main__": |
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282 unittest.TextTestRunner(verbosity=2).run( test_suite ) |