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1 import unittest
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2 import os, os.path, glob
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3 from SMART.Java.Python.GetDifferentialExpression import GetDifferentialExpression
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4
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5
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6 class Test_F_GetDifferentialExpression(unittest.TestCase):
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7
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8 def setUp(self):
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9 self.inputFileName1 = "inputFile1.gff3"
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10 self.inputFileName2 = "inputFile2.gff3"
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11 self.refFileName = "refFile.gff3"
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12 self.outputFileName = "outputFile.gff3"
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13 self.plotFileName = "outputFile.png"
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14
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15 def tearDown(self):
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16 for fileRoot in (self.inputFileName1, self.inputFileName2, self.refFileName, self.outputFileName, self.plotFileName):
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17 for file in glob.glob("%s*" % (fileRoot)):
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18 os.remove(file)
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19 os.remove(".RData")
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20
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21 def test_run_simple(self):
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22 handle = open(self.inputFileName1, "w")
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23 handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1;nbElements=100\n")
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24 handle.write("chr2\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test2;Name=test2;nbElements=1000\n")
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25 handle.close()
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26 handle = open(self.inputFileName2, "w")
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27 handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1;nbElements=200\n")
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28 handle.write("chr2\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test2;Name=test2;nbElements=1000\n")
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29 handle.close()
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30 handle = open(self.refFileName, "w")
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31 handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1")
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32 handle.close()
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33 differentialExpression = GetDifferentialExpression(0)
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34 differentialExpression.setInputFile(0, self.inputFileName1, "gff3")
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35 differentialExpression.setInputFile(1, self.inputFileName2, "gff3")
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36 differentialExpression.setReferenceFile(self.refFileName, "gff3")
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37 differentialExpression.setOutputFile(self.outputFileName)
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38 differentialExpression.setPlotterName(self.plotFileName)
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39 differentialExpression.setPlotter()
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40 differentialExpression.getDifferentialExpression()
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41 differentialExpression.mySqlConnection.deleteDatabase()
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42 handle = open(self.outputFileName)
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43 lines = handle.readlines()
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44 self.assertEquals(len(lines), 1)
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45 self.assertEquals(lines[0], "chr1\tS-MART\ttranscript\t1000\t2000\t.\t+\t.\tnbReadsCond1=100;nbReadsCond2=200;ID=test1;regulation=up;nbUnnormalizedReadsCond2=200;nbUnnormalizedReadsCond1=100;pValue=6.010045e-08;Name=test1\n")
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46 self.assertTrue(os.path.exists(self.plotFileName))
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47
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48 if __name__ == "__main__":
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49 unittest.main()
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50
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