Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/structure/test/Test_SubMapping.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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diff changeset
1 import unittest
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 from SMART.Java.Python.structure.Interval import Interval
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3 from SMART.Java.Python.structure.SubMapping import SubMapping
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4
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5 class Test_SubMapping(unittest.TestCase):
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6
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7 def test__init__(self):
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8 expEvalue = 0.00
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9 expScore = 0
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10 expIdentity = 0.00
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11 expTargetInterval = Interval()
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12 expQueryInterval = Interval()
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13 expQueryRange = expQueryInterval
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14 expSubjectRange = expTargetInterval
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15 expSize = None
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16 expTags = {}
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17
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18 iSubMapping = SubMapping()
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19 obsQueryRange = iSubMapping.getQueryAsRange()
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20 obsSubjectRange = iSubMapping.getSubjectAsRange()
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21 obsEvalue = iSubMapping.getEvalue()
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22 obsScore = iSubMapping.getScore()
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23 obsIdentity = iSubMapping.getIdentity()
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24 obsTargetInterval = iSubMapping.getTargetInterval()
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25 obsQueryInterval = iSubMapping.getQueryInterval()
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26 obsSize = iSubMapping.getSize()
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27 obsTags = iSubMapping.getTags()
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28
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29 self.assertEquals(expEvalue, obsEvalue)
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30 self.assertEquals(expIdentity, obsIdentity)
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31 self.assertEquals(expQueryInterval, obsQueryInterval)
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32 self.assertEquals(expQueryRange, obsQueryRange)
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33 self.assertEquals(expScore, obsScore)
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34 self.assertEquals(expSize, obsSize)
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35 self.assertEquals(expSubjectRange, obsSubjectRange)
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36 self.assertEquals(expTags, obsTags)
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37 self.assertEquals(expTargetInterval, obsTargetInterval)
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38
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39 def test__init__change_values_by_Interval(self):
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40 iSubMapping = SubMapping()
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41
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42 expSeqName = ""
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43
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44 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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45 obsRangeQuery = iSubMapping.range_query.getSeqname()
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46 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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47 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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48
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49 self.assertEquals(expSeqName, obsRangeSubject)
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50 self.assertEquals(expSeqName, obsRangeQuery)
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51 self.assertEquals(expSeqName, obsIntervalTarget)
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52 self.assertEquals(expSeqName, obsIntervalQuery)
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53
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54 iSubMapping.getTargetInterval().setChromosome("intervalTarget")
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55 iSubMapping.getQueryInterval().setChromosome("intervalQuery")
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56
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57 expTargetSeqName = "intervalTarget"
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58 expQuerySeqName = "intervalQuery"
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59
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60 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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61 obsRangeQuery = iSubMapping.range_query.getSeqname()
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62 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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63 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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64
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65 self.assertEquals(expTargetSeqName, obsRangeSubject)
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66 self.assertEquals(expQuerySeqName, obsRangeQuery)
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67 self.assertEquals(expTargetSeqName, obsIntervalTarget)
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68 self.assertEquals(expQuerySeqName, obsIntervalQuery)
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69
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70 def test__init__change_values_by_Align(self):
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71 iSubMapping = SubMapping()
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72
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73 expSeqName = ""
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74
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75 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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76 obsRangeQuery = iSubMapping.range_query.getSeqname()
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77 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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78 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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79
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80 self.assertEquals(expSeqName, obsRangeSubject)
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81 self.assertEquals(expSeqName, obsRangeQuery)
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82 self.assertEquals(expSeqName, obsIntervalTarget)
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83 self.assertEquals(expSeqName, obsIntervalQuery)
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84
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85 iSubMapping.range_subject.setSeqName("intervalTarget")
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86 iSubMapping.range_query.setSeqName("intervalQuery")
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87
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88 expTargetSeqName = "intervalTarget"
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89 expQuerySeqName = "intervalQuery"
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90
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91 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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92 obsRangeQuery = iSubMapping.range_query.getSeqname()
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93 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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94 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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95
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96 self.assertEquals(expTargetSeqName, obsRangeSubject)
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97 self.assertEquals(expQuerySeqName, obsRangeQuery)
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98 self.assertEquals(expTargetSeqName, obsIntervalTarget)
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99 self.assertEquals(expQuerySeqName, obsIntervalQuery)
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100
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101 def test__eq__(self):
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102 iSubMapping1 = SubMapping()
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103 iSubMapping1.setQueryName("Query")
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104 iSubMapping1.setQueryStart(50)
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105 iSubMapping1.setQueryEnd(150)
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106 iSubMapping1.setSubjectName("Subject")
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107 iSubMapping1.setSubjectStart(100)
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108 iSubMapping1.setSubjectEnd(200)
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109 iSubMapping1.e_value = 1e-20
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110 iSubMapping1.score = 30
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111 iSubMapping1.identity = 90.2
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112 iInterval1 = Interval()
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113 iInterval1.setChromosome("chromosome1")
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114 iInterval1.setStart(0)
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115 iInterval1.setEnd(100)
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116 iInterval1.setDirection("+")
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117 iInterval2 = Interval()
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118 iInterval2.setChromosome("chromosome2")
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119 iInterval2.setStart(200)
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120 iInterval2.setEnd(300)
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121 iInterval2.setDirection("+")
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122 iSubMapping1.setTargetInterval(iInterval1)
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123 iSubMapping1.setQueryInterval(iInterval2)
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124 iSubMapping1.setTagValue("name", 50)
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125 iSubMapping1.setSize(100)
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126
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127 iSubMapping2 = SubMapping()
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128 iSubMapping2.setQueryName("Query")
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129 iSubMapping2.setQueryStart(50)
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130 iSubMapping2.setQueryEnd(150)
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yufei-luo
parents:
diff changeset
131 iSubMapping2.setSubjectName("Subject")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
132 iSubMapping2.setSubjectStart(100)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
133 iSubMapping2.setSubjectEnd(200)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
134 iSubMapping2.e_value = 1e-20
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
135 iSubMapping2.score = 30
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
136 iSubMapping2.identity = 90.2
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
137 iSubMapping2.setTargetInterval(iInterval1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
138 iSubMapping2.setQueryInterval(iInterval2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
139 iSubMapping2.setTagValue("name", 50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
140 iSubMapping2.setSize(100)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
141 self.assertEqual(iSubMapping1, iSubMapping2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
142
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
143
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
144 def test__eq__withInitialValue(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
145 iSubMapping1 = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
146 iInterval1 = Interval()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
147 iInterval2 = Interval()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
148 iSubMapping1.setTargetInterval(iInterval1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
149 iSubMapping1.setQueryInterval(iInterval2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
150 iSubMapping1.setTagValue("name", 50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
151 iSubMapping1.setSize(100)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
152
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
153 iSubMapping2 = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
154 iSubMapping2.setTargetInterval(iInterval1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
155 iSubMapping2.setQueryInterval(iInterval2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
156 iSubMapping2.setTagValue("name", 50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
157 iSubMapping2.setSize(100)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
158 self.assertEqual(iSubMapping1, iSubMapping2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
159
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
160
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
161 def test__init__with_copy(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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162 iTestSubMapping = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
163 iTestSubMapping.setQueryName("Query")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
164 iTestSubMapping.setQueryStart(50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
165 iTestSubMapping.setQueryEnd(150)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
166 iTestSubMapping.setSubjectName("Subject")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
167 iTestSubMapping.setSubjectStart(100)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
168 iTestSubMapping.setSubjectEnd(200)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
169 iTestSubMapping.e_value = 1e-20
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
170 iTestSubMapping.score = 30
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
171 iTestSubMapping.identity = 90.2
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
172
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
173 iIntervalTarget = Interval()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
174 iIntervalTarget.setChromosome("chromosomeTarget")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
175 iIntervalTarget.setName("sequenceTarget")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
176 iIntervalTarget.setStart(0)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
177 iIntervalTarget.setEnd(123)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
178 iIntervalTarget.setDirection("+")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
179 iIntervalQuery = Interval()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
180 iIntervalQuery.setChromosome("chromosomeQuery")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
181 iIntervalQuery.setName("sequenceQuery")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
182 iIntervalQuery.setStart(200)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
183 iIntervalQuery.setEnd(323)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
184 iIntervalQuery.setDirection("+")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
185
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
186 iTestSubMapping.setQueryInterval(iIntervalTarget)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
187 iTestSubMapping.setTargetInterval(iIntervalQuery)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
188 iTestSubMapping.setTagValue("identity", 50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
189 iTestSubMapping.setSize(10)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
190
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
191 iSubMappingWithCopy = SubMapping(iTestSubMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
192 self.assertEquals(iSubMappingWithCopy, iTestSubMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
193
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
194
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
195 def test_copy(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
196 iSubMapping = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
197 iSubMapping.setQueryName("Query")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
198 iSubMapping.setQueryStart(50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
199 iSubMapping.setQueryEnd(150)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
200 iSubMapping.setSubjectName("Subject")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
201 iSubMapping.setSubjectStart(100)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
202 iSubMapping.setSubjectEnd(200)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
203 iSubMapping.e_value = 1e-20
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
204 iSubMapping.score = 30
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
205 iSubMapping.identity = 90.2
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
206
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
207 iInterval1 = Interval()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
208 iInterval1.setChromosome("chromosome1")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
209 iInterval1.setName("sequence1")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
210 iInterval1.setStart(0)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
211 iInterval1.setEnd(123)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
212 iInterval1.setDirection("+")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
213 iInterval2 = Interval()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
214 iInterval2.setChromosome("chromosome2")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
215 iInterval2.setName("sequence2")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
216 iInterval2.setStart(200)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
217 iInterval2.setEnd(300)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
218 iInterval2.setDirection("+")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
219 iSubMapping.setQueryInterval(iInterval1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
220 iSubMapping.setTargetInterval(iInterval2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
221 iSubMapping.setTagValue("identity", 50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
222 iSubMapping.setSize(10)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
223
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
224 iSubMappingCopy = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
225 iSubMappingCopy.copy(iSubMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
226 self.assertEqual(iSubMappingCopy, iSubMapping)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
227
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
228
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
229 def test_setTags(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
230 iSubMapping = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
231 iSubMapping.getQueryInterval().setSize(50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
232 iSubMapping.getTargetInterval().setSize(2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
233 iSubMapping.setTagValue("identity", 50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
234 iSubMapping.setSize(10)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
235
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
236 expQueryIntervalSize = 50
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
237 expTargetIntervalSize = 2
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
238 expTags = {"identity" : 50,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
239 "nbMismatches" : 5}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
240
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
241 obsTags = iSubMapping.getTags()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
242 self.assertEquals(expTags, obsTags)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
243
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
244
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
245 def test_setIdentity(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
246 iSubMapping = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
247 iSubMapping.setIdentity(10)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
248 expIdentity = 10
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
249 expTags = {"identity": 10}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
250
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
251 obsIdentity = iSubMapping.getIdentity()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
252 obsTags = iSubMapping.getTags()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
253
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
254 self.assertEquals(expIdentity,obsIdentity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
255 self.assertEquals(expTags,obsTags)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
256
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
257
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
258 def test_setIdentity_with_size(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
259 iSubMapping = SubMapping()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
260 iSubMapping.setSize(10)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
261 iSubMapping.setIdentity(50)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
262
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
263 expIdentity = 50
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
264 expTags = {"identity" : 50,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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265 "nbMismatches" : 5}
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266
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267 obsIdentity = iSubMapping.getIdentity()
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268 obsTags = iSubMapping.getTags()
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269
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270 self.assertEquals(expIdentity,obsIdentity)
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271 self.assertEquals(expTags,obsTags)
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272
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273
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274 def test_setIdentity_with_sizeAndMismatchTag(self):
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275 iSubMapping = SubMapping()
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276 iSubMapping.setSize(10)
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277 iSubMapping.setTagValue("nbMismatches", 8)
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278 iSubMapping.setIdentity(50)
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279
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280 expIdentity = 50
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281 expTags = {"identity" : 50,
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282 "nbMismatches" : 8}
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283
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284 obsIdentity = iSubMapping.getIdentity()
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285 obsTags = iSubMapping.getTags()
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286
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287 self.assertEquals(expIdentity,obsIdentity)
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288 self.assertEquals(expTags,obsTags)
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289
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290
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291 if __name__ == "__main__":
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292 unittest.main()