Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/coord/test/Test_MergedRange.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
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children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 from commons.core.coord.MergedRange import MergedRange
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3 from commons.core.coord.Match import Match
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4
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5 class Test_MergedRange(unittest.TestCase):
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7 def test_eq_True(self):
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8 mr1 = MergedRange([1], 6, 10)
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9 mr2 = MergedRange([1], 6, 10)
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10 self.assertEquals(mr1, mr2)
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11
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12 def test_eq_different_list(self):
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13 mr1 = MergedRange([1], 6, 10)
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14 mr2 = MergedRange([1, 2], 6, 10)
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15 self.assertNotEquals(mr1, mr2)
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16
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17 def test_eq_different_start(self):
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18 mr1 = MergedRange([1], 5, 10)
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19 mr2 = MergedRange([1], 6, 10)
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20 self.assertNotEquals(mr1, mr2)
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22 def test_eq_different_end(self):
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23 mr1 = MergedRange([1], 6, 10)
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24 mr2 = MergedRange([1], 6, 11)
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25 self.assertNotEquals(mr1, mr2)
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26
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27 def test_isOverlapping_no( self ):
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28 mr1 = MergedRange([1], 6, 10)
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29 mr2 = MergedRange([2], 16, 20)
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30 exp = False
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31 obs = mr1.isOverlapping( mr2 )
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32 self.assertEquals( exp, obs )
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33
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34 def test_isOverlapping_yes( self ):
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35 mr1 = MergedRange([1], 6, 10)
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36 mr2 = MergedRange([2], 5, 20)
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37 exp = True
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38 obs = mr1.isOverlapping( mr2 )
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39 self.assertEquals( exp, obs )
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40
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41 def test_isOverlapping_range1_before_range2( self ):
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42 mr1 = MergedRange([1], 6, 10)
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43 mr2 = MergedRange([2], 8, 15)
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44 exp = True
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45 obs = mr1.isOverlapping( mr2 )
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46 self.assertEquals( exp, obs )
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47
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48 def test_isOverlapping_range1_after_range2( self ):
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49 mr1 = MergedRange([1], 6, 10)
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50 mr2 = MergedRange([2], 1, 8)
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51 exp = True
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52 obs = mr1.isOverlapping( mr2 )
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53 self.assertEquals( exp, obs )
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54
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55 def test_isOverlapping_range1_equal_range2( self ):
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56 mr1 = MergedRange([1], 6, 10)
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57 mr2 = MergedRange([2], 6, 10)
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58 exp = True
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59 obs = mr1.isOverlapping( mr2 )
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60 self.assertEquals( exp, obs )
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61
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62 def test_merge_mr1_with_mr2(self):
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63 otherMergedRange = MergedRange()
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64 otherMergedRange._lId.append(3)
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65 otherMergedRange._start = 1
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66 otherMergedRange._end = 10
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67
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68 mr1 = MergedRange()
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69 mr1._lId.append(1)
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70 mr1._start = 6
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71 mr1._end = 10
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72
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73 mr2 = MergedRange([2], 1, 15)
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74 mr1.merge(mr2)
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75
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76 exp = MergedRange([1, 2], 1, 15)
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77 self.assertEquals(exp, mr1)
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78
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79 def test_merge_mr2_with_mr1(self):
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80 mr1 = MergedRange([1], 6, 10)
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81 mr2 = MergedRange([2], 1, 15)
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82 mr2.merge(mr1)
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83 exp = MergedRange([1, 2], 1, 15)
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84 self.assertEquals(exp, mr2)
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85
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86 def test_setFromMatch(self):
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87 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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88 iMatch = Match()
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89 iMatch.setFromTuple(tuple)
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90
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91 expMergedRange = MergedRange([1], 1, 5)
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92 obsMergedRange = MergedRange()
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93 obsMergedRange.setFromMatch(iMatch)
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94
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95 self.assertEquals(expMergedRange, obsMergedRange)
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96
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97 def test_getMergedRangeListFromMatchList(self):
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98 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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99 iMatch1 = Match()
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100 iMatch1.setFromTuple(tuple1)
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101 tuple2 = ("QName", 10, 15, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 2)
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102 iMatch2 = Match()
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103 iMatch2.setFromTuple(tuple2)
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104 lMatch = [iMatch1, iMatch2]
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105
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106 explMergedRange = [MergedRange([1], 1, 5), MergedRange([2], 10, 15)]
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107 obslMergedRange = MergedRange.getMergedRangeListFromMatchList(lMatch)
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108
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109 self.assertEquals(explMergedRange, obslMergedRange)
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110
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111 def test_getMergedRangeListFromMatchList_empty_list(self):
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112 lMatch = []
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113 explMergedRange = []
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114 obslMergedRange = MergedRange.getMergedRangeListFromMatchList(lMatch)
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115
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116 self.assertEquals(explMergedRange, obslMergedRange)
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117
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118 if __name__ == "__main__":
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119 unittest.main()