Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/ncList/test/Test_FindOverlapsWithSeveralIntervals.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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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
1 import unittest
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
2 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 from SMART.Java.Python.ncList.FindOverlapsWithSeveralIntervals import FindOverlapsWithSeveralIntervals
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4
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5 class Test_FindOverlapsWithSeveralIntervals(unittest.TestCase):
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6
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7 def setUp(self):
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8 self._inputRefGff3FileName = 'sortedFile.gff3'
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9 self._writeGFF3File(self._inputRefGff3FileName)
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10 self._inputQueryGff3FileName = 'sorted_Query.gff3'
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 self._writeQueryGff3File(self._inputQueryGff3FileName)
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12 self._outputGff3FileName = 'overlaps.gff3'
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 self._iFOWSI = FindOverlapsWithSeveralIntervals(self._inputRefGff3FileName, self._inputQueryGff3FileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 self._iFOWSI.setOutputGff3FileName(self._outputGff3FileName)
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15
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16 def tearDown(self):
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17 os.remove(self._inputRefGff3FileName)
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18 os.remove(self._inputQueryGff3FileName)
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19 os.remove(self._outputGff3FileName)
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20 self._iFOWSI.deletIntermediateFiles()
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21
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22 def test_isOverlapping_true(self):
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23 queryGff3Addr = 116
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24 RefGff3Addr = 231
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25 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr)
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26 exp = 0
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27 self.assertEquals(exp, obs)
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28
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29 def test_isOverlapping_false_left(self):
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30 queryGff3Addr = 116
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31 RefGff3Addr = 58
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32 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr)
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33 exp = -1
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34 self.assertEquals(exp, obs)
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35
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36 def test_isOverlapping_false_right(self):
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37 queryGff3Addr = 116
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38 RefGff3Addr = 347
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39 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr)
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40 exp = 1
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41 self.assertEquals(exp, obs)
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42
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43 def test_getHisFirstChild(self):
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44 firstRefLAddr = 0
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45 obsFirstChildLAddr = self._iFOWSI.getHisFirstChild(firstRefLAddr)
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46 expFirstChildLAddr = 48
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47 self.assertEquals(expFirstChildLAddr, obsFirstChildLAddr)
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48
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49 def test_isLastElement_true(self):
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50 refLAddr = 96
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51 obsBool = self._iFOWSI.isLastElement(refLAddr)
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52 expBool = True
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53 self.assertEquals(expBool, obsBool)
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54
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55 def test_isLastElement_false(self):
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56 refLAddr = 72
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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57 obsBool = self._iFOWSI.isLastElement(refLAddr)
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58 expBool = False
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59 self.assertEquals(expBool, obsBool)
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60
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61 def test_isLastElement_highestLevel_true(self):
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62 refLAddr = 24
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63 obsBool = self._iFOWSI.isLastElement(refLAddr)
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64 expBool = True
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65 self.assertEquals(expBool, obsBool)
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66
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67 def test_isLastElement_highestLevel_false(self):
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68 refLAddr = 0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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69 obsBool = self._iFOWSI.isLastElement(refLAddr)
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70 expBool = False
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71 self.assertEquals(expBool, obsBool)
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72
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73 def test_findOverlapIter(self):
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74 queryGff3Addr = 175
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75 firstRefLAddr = 0
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76 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr)
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77 expFirstOverlapLAddr = 0
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78 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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79
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80 def test_not_findOverlapIter(self):
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81 queryGff3Addr = 295
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82 firstRefLAddr = 24
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83 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr)
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84 expFirstOverlapLAddr = None
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85 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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86
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87 def test_findOverlapIter_not_the_first_RefOverlap(self):
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88 queryGff3Addr = 235
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89 firstRefLAddr = 0
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90 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr)
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91 expFirstOverlapLAddr = 24
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92 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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93
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94 def test_changeToNewSubEndLAddr(self):
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95 firstChildLAddr = 48
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96 subEndLAddr = 48
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97 expSubEndLAddr = 120
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98 obsSubEndLAddr = self._iFOWSI.changeToNewSubEndLAddr(firstChildLAddr, subEndLAddr)
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99 self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
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100
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101 def test_defineSubEndLaddr(self):
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102 parentLAddr = -1
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103 expSubEndLAddr = 48
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104 obsSubEndLAddr = self._iFOWSI.defineSubEndLaddr(parentLAddr)
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105 self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
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106
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107 def test_getNextRefIntervalInCaseNotOverLap(self):
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108 firstRefLAddr = 96
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109 expRefLAddr = 24
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110 obsRefLAddr = self._iFOWSI.getNextRefIntervalInCaseNotOverLap(firstRefLAddr)
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111 self.assertEquals(expRefLAddr, obsRefLAddr)
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112
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113 def test_getNextRefIntervalInCaseOverLap(self):
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114 firstChildLAddr = -1
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115 firstRefLAddr = 120
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116 subEndLAddr = 144
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117 expRefLAddr, expSubEndLAddr = (96, 144)
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118 obsRefLAddr, obsSubEndLAddr = self._iFOWSI.getNextRefIntervalInCaseOverLap(firstChildLAddr, firstRefLAddr, subEndLAddr)
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119 self.assertEquals((expRefLAddr, expSubEndLAddr), (obsRefLAddr, obsSubEndLAddr))
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120
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121 def test_not_findOverlapIter_between2RefIntervals(self):
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122 inputQueryGff3FileName = 'query2.gff3'
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123 self._writeQueryGff3File2(inputQueryGff3FileName)
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124 self._iFOWSI.setQueryGff3FileName(inputQueryGff3FileName)
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125 queryGff3Addr = 0
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126 firstRefLAddr = 0
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127 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr)
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128 expFirstOverlapLAddr = 24
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129 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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130 os.remove(inputQueryGff3FileName)
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131
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132 def _writeQueryGff3File2(self, fileName):
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133 f = open(fileName, 'w')
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134 f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
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135 f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=test1.2;Name=test1.2\n")
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136 f.close()
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137
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138 def _writeQueryGff3File(self, fileName):
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139 f = open(fileName, 'w')
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140 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
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141 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=test1.2;Name=test1.2\n")
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142 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=test1.3;Name=test1.3\n")
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143 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=test1.4;Name=test1.4\n")
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144 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=test1.5;Name=test1.5\n")
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145 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=test1.6;Name=test1.6\n")
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146 f.close()
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147
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148 def _writeGFF3File(self, fileName):
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149 f = open(fileName, "w")
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150 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
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151 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
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152 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
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153 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
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154 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
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155 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
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156 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
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157 f.close()
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158
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159 if __name__ == "__main__":
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160 unittest.main()