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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 import sys
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35 from commons.core.coord.MapUtils import MapUtils
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36 from commons.core.coord.Map import Map
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37 from commons.core.coord.Set import Set
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38 from commons.core.utils.FileUtils import FileUtils
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39
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40
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41 class Test_MapUtils( unittest.TestCase ):
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42
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43 def test_getMapListSortedByIncreasingMinThenMax( self ):
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44 iMap1 = Map("name1", "chr1", 1, 350)
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45 iMap2 = Map("name2", "chr1", 1, 100)
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46 iMap3 = Map("name3", "chr1", 50, 350)
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47 iMap4 = Map("name4", "chr1", 5, 450)
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48 lMaps = [ iMap1, iMap2, iMap3, iMap4 ]
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49
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50 expLMaps = [ iMap2, iMap1, iMap4, iMap3 ]
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51
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52 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
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53
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54 self.assertEquals( expLMaps, obsLMaps )
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55
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56
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57 def test_getMapListSortedByIncreasingMinThenMax_ordered( self ):
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58 iMap1 = Map("name1", "chr1", 1, 100)
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59 iMap2 = Map("name2", "chr1", 1, 350)
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60
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61 lMaps = [ iMap1, iMap2 ]
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62 expLMaps = [ iMap1, iMap2 ]
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63
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64 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
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65
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66 self.assertEquals( expLMaps, obsLMaps )
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67
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68
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69 def test_getMapListSortedByIncreasingMinThenMax_unordered( self ):
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70 iMap1 = Map("name1", "chr1", 1, 350)
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71 iMap2 = Map("name2", "chr1", 1, 100)
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72
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73 lMaps = [ iMap1, iMap2 ]
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74 expLMaps = [ iMap2, iMap1 ]
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75
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76 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
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77
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78 self.assertEquals( expLMaps, obsLMaps )
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79
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80
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81 def test_getMapListSortedByIncreasingMinThenMax_nonOverlapping( self ):
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82 iMap1 = Map("name1", "chr1", 1, 350)
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83 iMap2 = Map("name2", "chr1", 400, 600)
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84
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85 lMaps = [ iMap2, iMap1 ]
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86 expLMaps = [ iMap1, iMap2 ]
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87
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88 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
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89
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90 self.assertEquals( expLMaps, obsLMaps )
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91
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92
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93 def test_getMapListSortedByIncreasingMinThenMax_sameMinThreeMaps( self ):
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94 iMap1 = Map("name1", "chr1", 350, 1)
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95 iMap2 = Map("name2", "chr1", 400, 1)
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96 iMap3 = Map("name3", "chr1", 500, 1)
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97
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98 lMaps = [ iMap2, iMap1, iMap3 ]
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99 expLMaps = [ iMap1, iMap2, iMap3 ]
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100
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101 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
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102
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103 self.assertEquals( expLMaps, obsLMaps )
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104
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105
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106 def test_getMapListSortedByIncreasingMinThenMax_included( self ):
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107 iMap1 = Map("name1", "chr1", 350, 1)
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108 iMap2 = Map("name2", "chr1", 300, 10)
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109
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110 lMaps = [ iMap2, iMap1 ]
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111 expLMaps = [ iMap1, iMap2]
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112
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113 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
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114
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115 self.assertEquals( expLMaps, obsLMaps )
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116
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117
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118 def test_getMapListSortedByIncreasingMinThenMax_equal( self ):
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119 iMap1 = Map("name1", "chr1", 350, 1)
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120 iMap2 = Map("name2", "chr1", 350, 1)
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121
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122 lMaps = [ iMap2, iMap1 ]
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123 expLMaps = [ iMap2, iMap1 ]
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124 notExpLMaps = [ iMap1, iMap2 ]
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125
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126 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
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127
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128 self.assertEquals( expLMaps, obsLMaps )
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129 self.assertNotEquals( notExpLMaps, obsLMaps )
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130
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131
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132 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( self ):
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133 iMap1 = Map("name1", "chr1", 1, 350)
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134 iMap2 = Map("name4", "chr2", 5, 450)
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135 iMap3 = Map("name4", "chr1", 10, 450)
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136 iMap4 = Map("name4", "chr1", 10, 500)
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137 iMap5 = Map("name4", "chr1", 5, 450)
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138 iMap6 = Map("name3", "chr1", 50, 350)
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139 iMap7 = Map("name2", "chr1", 1, 100)
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140
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141 lMaps = [ iMap1, iMap2, iMap3, iMap4, iMap5, iMap6, iMap7 ]
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142
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143 expLMaps = [ iMap1, iMap7, iMap6, iMap5, iMap3, iMap4, iMap2 ]
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144
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145 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
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146
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147 self.assertEquals( expLMaps, obsLMaps )
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148
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149
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150 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_ordered( self ):
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151 iMap1 = Map("name1", "chr1", 1, 100)
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152 iMap2 = Map("name1", "chr2", 1, 350)
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153
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154 lMaps = [ iMap1, iMap2 ]
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155 expLMaps = [ iMap1, iMap2 ]
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156
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157 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
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158
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159 self.assertEquals( expLMaps, obsLMaps )
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160
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161
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162 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_unordered( self ):
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163 iMap1 = Map("name1", "chr2", 1, 350)
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164 iMap2 = Map("name1", "chr1", 1, 100)
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165
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166 lMaps = [ iMap1, iMap2 ]
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167 expLMaps = [ iMap2, iMap1 ]
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168
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169 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
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170
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171 self.assertEquals( expLMaps, obsLMaps )
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172
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173
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174 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_nonOverlapping( self ):
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175 iMap1 = Map("name1", "chr1", 1, 350)
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176 iMap2 = Map("name2", "chr1", 400, 600)
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177
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178 lMaps = [ iMap2, iMap1 ]
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179 expLMaps = [ iMap1, iMap2 ]
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180
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181 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
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182
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183 self.assertEquals( expLMaps, obsLMaps )
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184
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185
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186 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_sameMinThreeMaps( self ):
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187 iMap1 = Map("name2", "chr1", 150, 10)
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188 iMap2 = Map("name2", "chr1", 1, 100)
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189 iMap3 = Map("name2", "chr1", 100, 1)
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190
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191 lMaps = [ iMap1, iMap2, iMap3 ]
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192 expLMaps = [ iMap2, iMap3, iMap1 ]
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193
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194 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
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195
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196 self.assertEquals( expLMaps, obsLMaps )
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197
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198
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199 def test_getDictPerNameFromMapFile( self ):
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200 iMap1 = Map( "chunk1", "chromosome1", 1, 100 )
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201 iMap2 = Map( "chunk2", "chromosome1", 91, 190 )
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202 iMap3 = Map( "chunk3", "chromosome2", 1, 100 )
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203 iMap4 = Map( "chunk1", "chromosome1", 1, 100 ) # redundant with iMap1
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204
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205 mapFile = "dummyFile.map"
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206 mapFileHandler = open( mapFile, "w" )
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207 for iMap in [ iMap1, iMap2, iMap3, iMap4 ]:
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208 iMap.write( mapFileHandler )
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209 mapFileHandler.close()
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210
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211 dExp = { "chunk1": iMap1, "chunk2": iMap2, "chunk3": iMap3 }
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212
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213 dObs = MapUtils.getDictPerNameFromMapFile( mapFile )
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214
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215 self.assertEquals( dExp, dObs )
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216
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217 os.remove( mapFile )
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218
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219
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220 def test_mapList2SetList(self):
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221 map1 = Map( "name1", "desc1", 1, 120 )
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222 map2 = Map( "name2", "desc2", 1, 20 )
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223 lMap = [ map1, map2 ]
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224 set1 = Set( 1, "name1", "desc1", 1, 120 )
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225 set2 = Set( 2, "name2", "desc2", 1, 20 )
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226 explMapSet = [ set1, set2 ]
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227 obslMapSet = MapUtils.mapList2SetList( lMap )
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228
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229 self.assertEquals( explMapSet, obslMapSet )
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230
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231
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232 def test_mergeCoordsInFile( self ):
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233 if sys.modules.has_key( "commons.core.checker.CheckerUtils" ):
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234 inFile = "dummyInFile"
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235 inFileHandler = open( inFile, "w" )
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236 inFileHandler.write( "TE1\tchr1\t1501\t2500\n" )
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237 inFileHandler.write( "TE3\tchr1\t4000\t3401\n" )
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238 inFileHandler.write( "TE3\tchr1\t3800\t3601\n" )
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239 inFileHandler.close()
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240 expFile = "dummyExpFile"
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241 expFileHandler = open( expFile, "w" )
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242 expFileHandler.write( "TE1\tchr1\t1501\t2500\n" )
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243 expFileHandler.write( "TE3\tchr1\t4000\t3401\n" )
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244 expFileHandler.close()
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245 obsFile = "dummyObsFile"
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246 MapUtils.mergeCoordsInFile( inFile, obsFile )
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247 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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248 for f in [ inFile, expFile, obsFile ]:
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249 os.remove( f )
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250
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251
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252 def test_getDictPerSeqNameFromMapFile( self ):
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253 inFile = "dummyInFile"
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254 inFileHandler = open( inFile, "w" )
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255 inFileHandler.write( "TE1\tchr1\t1\t10\n" )
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256 inFileHandler.write( "TE2\tchr1\t60\t41\n" )
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257 inFileHandler.write( "TE3\tchr2\t5\t36\n" )
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258 inFileHandler.close()
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259 dExp = { "chr1": [ Map( "TE1", "chr1", 1, 10 ), Map( "TE2", "chr1", 60, 41 ) ],
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260 "chr2": [ Map( "TE3", "chr2", 5, 36 ) ] }
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261 dObs = MapUtils.getDictPerSeqNameFromMapFile( inFile )
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262 self.assertEqual( dExp, dObs )
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263 os.remove( inFile )
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264
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265 def test_convertMapFileIntoSetFile(self):
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266 mapInputFile = "dummyExpFile"
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267 mapFileHandler = open( mapInputFile, "w" )
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268 mapFileHandler.write( "seq31\tchr1\t151\t250\n" )
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269 mapFileHandler.write( "seq27\tchr2\t301\t500\n" )
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270 mapFileHandler.write( "seq40\tchr2\t600\t700\n" )
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271 mapFileHandler.write( "seq2\tchr3\t301\t500\n" )
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272 mapFileHandler.close()
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273
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274 expSetFile = "dummyexpSetFile"
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275 expSetFileHandler = open( expSetFile, "w" )
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276 expSetFileHandler.write( "1\tseq31\tchr1\t151\t250\n" )
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277 expSetFileHandler.write( "2\tseq27\tchr2\t301\t500\n" )
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278 expSetFileHandler.write( "3\tseq40\tchr2\t600\t700\n" )
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279 expSetFileHandler.write( "4\tseq2\tchr3\t301\t500\n" )
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280 expSetFileHandler.close()
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281
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282 obsFile = "dummyObsFile"
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283
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284 MapUtils.convertMapFileIntoSetFile( mapInputFile, obsFile )
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285
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286 self.assertTrue( FileUtils.are2FilesIdentical( expSetFile, obsFile ) )
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287
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288 for f in [ expSetFile, mapInputFile, obsFile ]:
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289 os.remove( f )
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290
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291 def test_convertMapFileIntoSetFile_one_line(self):
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292 mapInputFile = "dummyExpFile"
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293 mapFileHandler = open( mapInputFile, "w" )
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294 mapFileHandler.write( "seq31\tchr1\t151\t250\n" )
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295 mapFileHandler.close()
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296
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297 expSetFile = "dummyexpSetFile"
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298 expSetFileHandler = open( expSetFile, "w" )
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299 expSetFileHandler.write( "1\tseq31\tchr1\t151\t250\n" )
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300 expSetFileHandler.close()
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301
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302 obsFile = "dummyObsFile"
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303
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304 MapUtils.convertMapFileIntoSetFile( mapInputFile, obsFile )
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305
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306 self.assertTrue( FileUtils.are2FilesIdentical( expSetFile, obsFile ) )
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307
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308 for f in [ expSetFile, mapInputFile, obsFile ]:
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309 os.remove( f )
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310
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311 def test_convertMapFileIntoSetFile_empty_file(self):
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312 mapInputFile = "dummyFile.map"
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313 mapFileHandler = open( mapInputFile, "w" )
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314 mapFileHandler.close()
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315
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316 expFile = "dummyExpFile.map.set"
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317 expFileHandler = open( expFile, "w" )
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318 expFileHandler.close()
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319
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320 obsFile = "dummyFile.map.set"
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321
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322 MapUtils.convertMapFileIntoSetFile( mapInputFile )
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323
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324 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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325
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326 for f in [ expFile, mapInputFile, obsFile ]:
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327 os.remove( f )
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328
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329 def test_writeListInFile_empty_list(self):
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330 lMaps = [ ]
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331 expFileName = "expFileName"
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332 fileHandle = open(expFileName, "w")
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333 fileHandle.close()
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334
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335 obsFileName = "obsFileName"
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336 fileHandle = open(obsFileName, "w")
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337 MapUtils.writeListInFile(lMaps, obsFileName, "w")
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338 fileHandle.close()
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339
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340 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
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341
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342 os.remove(obsFileName)
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343 os.remove(expFileName)
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344
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345 def test_writeListInFile_list_one_set(self):
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346 lMaps = [ Map( "map1", "map1seq", 1, 10 ) ]
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347 line = "map1\tmap1seq\t1\t10\n"
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348
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349 expFileName = "expFileName"
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350
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351 fileHandle = open(expFileName, "w")
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352 fileHandle.write(line)
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353 fileHandle.close()
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354
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355 obsFileName = "obsFileName"
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356 fileHandle = open(obsFileName, "w")
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357 MapUtils.writeListInFile(lMaps, obsFileName, "w")
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358 fileHandle.close()
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359
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360 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
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361
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362 os.remove(obsFileName)
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363 os.remove(expFileName)
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364
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365 def test_getMinLengthOfMapFile(self):
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366 mapFileName = "%s/Gnome_tools/Vein_v4_scaffold_00001.fa.Nstretch.map" % os.environ["REPET_DATA"]
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367 expMinLengthofMapFile = 20
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368 iMap = MapUtils()
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369 obsMinLengthofMapFile = iMap.getMinLengthOfMapFile(mapFileName)
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370 self.assertEquals(expMinLengthofMapFile, obsMinLengthofMapFile)
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371
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372 def test_getMaxLengthOfMapFile(self):
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373 mapFileName = "%s/Gnome_tools/Vein_v4_scaffold_00001.fa.Nstretch.map" % os.environ["REPET_DATA"]
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374 expMinLengthofMapFile = 6344
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375 iMap = MapUtils()
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376 obsMinLengthofMapFile = iMap.getMaxLengthOfMapFile(mapFileName)
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377 self.assertEquals(expMinLengthofMapFile, obsMinLengthofMapFile)
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378
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379
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380
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381 test_suite = unittest.TestSuite()
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382 test_suite.addTest( unittest.makeSuite( Test_MapUtils ) )
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383 if __name__ == "__main__":
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384 unittest.TextTestRunner(verbosity=2).run( test_suite )
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