Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/coord/test/Test_Map.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
parents
children
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0
e0f8dcca02ed 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)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 #
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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.Map import Map
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35 from commons.core.utils.FileUtils import FileUtils
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36
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37
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38 class Test_Map( unittest.TestCase ):
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39
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40 def setUp(self):
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41 self._map = Map()
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42
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43 def test_setFromString(self):
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44 line = "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" # test with '\t' separator
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45 self._map.setFromString(line)
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46 self.assertEqual( self._map.name, "MbQ12Gr2Cl2" )
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47 self.assertEqual( self._map.seqname, "consensus1" )
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48 self.assertEqual( self._map.start, 51 )
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49 self.assertEqual( self._map.end, 1230 )
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50 line = "MbQ12Gr2Cl2;consensus1;51;1230" # test with ';' separator
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 self._map.setFromString(line,";")
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52 self.assertEqual( self._map.name, "MbQ12Gr2Cl2" )
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53 self.assertEqual( self._map.seqname, "consensus1" )
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54 self.assertEqual( self._map.start, 51 )
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55 self.assertEqual( self._map.end, 1230 )
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56
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57 def test___eq__(self):
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58 self._map.setFromString( "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" )
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59 o = Map()
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60 o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" )
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61 self.assertEqual( self._map, o ) # same data
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62 o.setFromString( "MbQ12Gr2Cl1\tconsensus1\t51\t1230\n" )
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63 self.assertNotEqual( self._map, o ) # different name
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64 o.setFromString( "MbQ12Gr2Cl2\tconsensus2\t51\t1230\n" )
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65 self.assertNotEqual( self._map, o ) # different seqname
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66 o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t15\t1230\n" )
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67 self.assertNotEqual( self._map, o ) # different start
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68 o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t51\t123000\n" )
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69 self.assertNotEqual( self._map, o ) # different end
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70 o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t1230\t51\n" )
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71 self.assertNotEqual( self._map, o ) # same start/end but in different order
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72
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73 def test_setFromTuple(self):
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74 tuple = ("MbQ12Gr2Cl2", "consensus1","51","1230")
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75 self._map.setFromTuple(tuple)
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76
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77 expMap = Map("MbQ12Gr2Cl2", "consensus1",51,1230)
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78 obsMap = self._map
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79
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80 self.assertEquals(expMap, obsMap)
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81
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82 def test_read_empty_file(self):
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83
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84 fileName = "dummyFile"
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85 os.system("touch " + fileName)
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86 fileHandle = open(fileName, "r")
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87
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88 obsResult = self._map.read(fileHandle)
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89 expResult = 0
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90
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91 fileHandle.close()
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92 os.remove(fileName)
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93
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94 self.assertEquals(expResult, obsResult)
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95
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96 def test_read_uncompleted_line( self):
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97 uncompletedLine = "MbQ12Gr2Cl2\tconsensus1\t51"
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98 fileName = "dummyFile"
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99
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100 fileHandle = open(fileName, "w")
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101 fileHandle.write(uncompletedLine)
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102 fileHandle.close()
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103
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104 fileHandle = open(fileName, "r")
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105
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106 obsResult = self._map.read(fileHandle)
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107 expResult = 0
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108
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109 fileHandle.close()
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110 os.remove(fileName)
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111
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112 self.assertEquals(obsResult, expResult)
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113
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114 def test_read(self):
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115 line = "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n"
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116 fileName = "dummyFile"
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117
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118 fileHandle = open(fileName, "w")
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119 fileHandle.write(line)
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120 fileHandle.close()
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121
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122 fileHandle = open(fileName, "r")
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123 self._map.read(fileHandle)
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124 obsResult = self._map
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125
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126 expResult = Map()
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127 expResult.setFromString(line)
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128
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129 fileHandle.close()
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130 os.remove(fileName)
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131
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132 self.assertEquals(obsResult, expResult)
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133
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134 def test_write(self):
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135 line = "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n"
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136 expFileName = "expFileName"
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137
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138 fileHandle = open(expFileName, "w")
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139 fileHandle.write(line)
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140 fileHandle.close()
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141
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142 obsFileName = "obsFileName"
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143 fileHandle = open(obsFileName, "w")
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144 self._map.setFromString(line)
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145 self._map.write(fileHandle)
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146 fileHandle.close()
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147
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148 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
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149
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150 os.remove(obsFileName)
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151 os.remove(expFileName)
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152
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153 def test_diff1(self):
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154 map1 = Map("seq1","DmelChr4", 190000, 390000)
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155 map2 = Map("seq2","DmelChr4", 290000, 590000)
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156
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157 expMap1 = Map("seq1", "DmelChr4", 190000, 289999)
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158 expReturnedMap = Map()
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159
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160 obsReturnedMap = map1.diff(map2)
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161 obsMap1 = map1
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162
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163 self.assertEquals(expMap1, obsMap1)
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164 self.assertEquals(expReturnedMap, obsReturnedMap)
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165
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166 def test_diff2(self):
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167 map1 = Map("seq1","DmelChr4", 190000, 590000)
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168 map2 = Map("seq2","DmelChr4", 290000, 390000)
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169
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170 expMap1 = Map("seq1", "DmelChr4", 190000, 289999)
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171 expReturnedMap = Map("seq1", "DmelChr4", 390001, 590000)
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172
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173 obsReturnedMap = map1.diff(map2)
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174 obsMap1 = map1
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175
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176 self.assertEquals(expMap1, obsMap1)
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177 self.assertEquals(expReturnedMap, obsReturnedMap)
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178
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179
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180 test_suite = unittest.TestSuite()
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181 test_suite.addTest( unittest.makeSuite( Test_Map ) )
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182 if __name__ == "__main__":
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183 unittest.TextTestRunner(verbosity=2).run( test_suite )