Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/mySql/test/Test_MySqlTranscriptTable.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.
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diff changeset
1 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
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2 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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3 from SMART.Java.Python.structure.Transcript import Transcript
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4 from SMART.Java.Python.structure.Interval import Interval
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 from SMART.Java.Python.mySql.MySqlConnection import MySqlConnection
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6 from SMART.Java.Python.mySql.MySqlTranscriptTable import MySqlTranscriptTable
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7 import unittest
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9
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10 class Test_MySqlTranscriptTable(unittest.TestCase):
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11
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12 def test_getRange(self):
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13 transcript = Transcript()
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14 transcript.setName("test1.1")
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15 transcript.setChromosome("arm_X")
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16 transcript.setStart(1000)
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17 transcript.setEnd(4000)
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18 transcript.setSize(2000)
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19 transcript.setDirection("+")
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20
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21 exon1 = Interval()
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22 exon1.setName("test1.1")
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23 exon1.setChromosome("arm_X")
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24 exon1.setStart(1000)
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25 exon1.setEnd(2000)
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26 exon1.setSize(1000)
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27
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28 exon2 = Interval()
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29 exon2.setName("test1.1")
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30 exon2.setChromosome("arm_X")
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31 exon2.setStart(3000)
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32 exon2.setEnd(4000)
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33 exon2.setSize(1000)
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34
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35 transcript.addExon(exon1)
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36 transcript.addExon(exon2)
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37
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38 connection = MySqlConnection()
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39 writer = MySqlTranscriptWriter(connection, "testMySqlTranscriptTableGetRange")
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40 writer.addTranscript(transcript)
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41 writer.write()
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42
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43 transcriptContainer = TranscriptContainer("testMySqlTranscriptTableGetRange", "sql")
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44 transcriptContainer.mySqlConnection = connection
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45 self.assertEqual(transcriptContainer.getNbTranscripts(), 1)
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46 for transcript in transcriptContainer.getIterator():
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47 self.assertEqual(transcript.getName(), "test1.1")
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48 self.assertEqual(transcript.getChromosome(), "arm_X")
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49 self.assertEqual(transcript.getStart(), 1000)
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50 self.assertEqual(transcript.getEnd(), 4000)
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51 self.assertEqual(transcript.getSize(), 2002)
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52 self.assertEqual(transcript.getNbExons(), 2)
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53 exons = transcript.getExons()
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54 self.assertEqual(exons[0].getStart(), 1000)
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55 self.assertEqual(exons[0].getEnd(), 2000)
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56 self.assertEqual(exons[1].getStart(), 3000)
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57 self.assertEqual(exons[1].getEnd(), 4000)
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58
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59
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60 def test_setDefaultTagValue(self):
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61 transcript1 = Transcript()
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62 transcript1.setName("test1.1")
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63 transcript1.setChromosome("arm_X")
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64 transcript1.setStart(1000)
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65 transcript1.setEnd(2000)
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66 transcript1.setDirection("+")
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67
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68 exon1 = Interval()
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69 exon1.setName("test1.1")
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70 exon1.setChromosome("arm_X")
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71 exon1.setStart(1000)
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72 exon1.setEnd(2000)
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73
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74 transcript1.addExon(exon1)
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75
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76 transcript2 = Transcript()
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77 transcript2.setName("test2.1")
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78 transcript2.setChromosome("arm_X")
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79 transcript2.setStart(1000)
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80 transcript2.setEnd(2000)
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81 transcript2.setDirection("+")
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82 transcript2.setTagValue("nbOccurrences", "2")
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83
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84 exon2 = Interval()
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85 exon2.setName("test2.1")
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86 exon2.setChromosome("arm_X")
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87 exon2.setStart(1000)
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88 exon2.setEnd(2000)
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89
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90 transcript2.addExon(exon2)
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91
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92 transcript3 = Transcript()
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93 transcript3.setName("test3.1")
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94 transcript3.setChromosome("arm_X")
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95 transcript3.setStart(1000)
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96 transcript3.setEnd(2000)
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97 transcript3.setDirection("+")
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98 transcript3.setTagValue("occurrences", "2")
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99
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100 exon3 = Interval()
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101 exon3.setName("test3.1")
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102 exon3.setChromosome("arm_X")
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103 exon3.setStart(1000)
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104 exon3.setEnd(2000)
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105
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106 transcript3.addExon(exon3)
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107
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108 connection = MySqlConnection()
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109 table = MySqlTranscriptTable(connection, "testMySqlTranscriptTableSetDefaultTagValue")
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110 table.createTranscriptTable()
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111 table.addTranscript(transcript1)
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112 table.addTranscript(transcript2)
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113 table.addTranscript(transcript3)
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114 table.setDefaultTagValue("occurrence", "1")
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115
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116 cpt = 0
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117 for transcript in table.getIterator():
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118 cpt += 1
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119 self.assert_(cpt != 4)
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120 if cpt == 1:
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121 self.assertEqual(transcript.name, "test1.1")
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122 self.assertEqual(transcript.getChromosome(), "arm_X")
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123 self.assertEqual(transcript.getStart(), 1000)
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124 self.assertEqual(transcript.getEnd(), 2000)
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125 self.assertEqual(transcript.getSize(), 1001)
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126 self.assertEqual(transcript.getNbExons(), 1)
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127 exons = transcript.getExons()
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128 self.assertEqual(exons[0].getStart(), 1000)
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129 self.assertEqual(exons[0].getEnd(), 2000)
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130 self.assertEqual(transcript.getTagValue("occurrence"), 1)
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131 elif cpt == 2:
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132 self.assertEqual(transcript.name, "test2.1")
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133 self.assertEqual(transcript.getChromosome(), "arm_X")
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134 self.assertEqual(transcript.getStart(), 1000)
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135 self.assertEqual(transcript.getEnd(), 2000)
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136 self.assertEqual(transcript.getSize(), 1001)
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137 self.assertEqual(transcript.getNbExons(), 1)
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138 exons = transcript.getExons()
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139 self.assertEqual(exons[0].getStart(), 1000)
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140 self.assertEqual(exons[0].getEnd(), 2000)
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141 self.assertEqual(transcript.getTagValue("nbOccurrences"), 2)
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142 self.assertEqual(transcript.getTagValue("occurrence"), 1)
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143 elif cpt == 2:
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144 self.assertEqual(transcript.name, "test3.1")
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145 self.assertEqual(transcript.getChromosome(), "arm_X")
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146 self.assertEqual(transcript.getStart(), 1000)
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147 self.assertEqual(transcript.getEnd(), 2000)
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148 self.assertEqual(transcript.getSize(), 1001)
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149 self.assertEqual(transcript.getNbExons(), 1)
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150 exons = transcript.getExons()
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151 self.assertEqual(exons[0].getStart(), 1000)
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152 self.assertEqual(exons[0].getEnd(), 2000)
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153 self.assertEqual(transcript.getTagValue("occurrence"), 2)
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154
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155 table.remove()
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156
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157 if __name__ == '__main__':
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158 unittest.main()