Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/test/Test_F_GetDifferentialExpression.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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import unittest import os, os.path, glob from SMART.Java.Python.GetDifferentialExpression import GetDifferentialExpression class Test_F_GetDifferentialExpression(unittest.TestCase): def setUp(self): self.inputFileName1 = "inputFile1.gff3" self.inputFileName2 = "inputFile2.gff3" self.refFileName = "refFile.gff3" self.outputFileName = "outputFile.gff3" self.plotFileName = "outputFile.png" def tearDown(self): for fileRoot in (self.inputFileName1, self.inputFileName2, self.refFileName, self.outputFileName, self.plotFileName): for file in glob.glob("%s*" % (fileRoot)): os.remove(file) os.remove(".RData") def test_run_simple(self): handle = open(self.inputFileName1, "w") handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1;nbElements=100\n") handle.write("chr2\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test2;Name=test2;nbElements=1000\n") handle.close() handle = open(self.inputFileName2, "w") handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1;nbElements=200\n") handle.write("chr2\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test2;Name=test2;nbElements=1000\n") handle.close() handle = open(self.refFileName, "w") handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1") handle.close() differentialExpression = GetDifferentialExpression(0) differentialExpression.setInputFile(0, self.inputFileName1, "gff3") differentialExpression.setInputFile(1, self.inputFileName2, "gff3") differentialExpression.setReferenceFile(self.refFileName, "gff3") differentialExpression.setOutputFile(self.outputFileName) differentialExpression.setPlotterName(self.plotFileName) differentialExpression.setPlotter() differentialExpression.getDifferentialExpression() differentialExpression.mySqlConnection.deleteDatabase() handle = open(self.outputFileName) lines = handle.readlines() self.assertEquals(len(lines), 1) 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") self.assertTrue(os.path.exists(self.plotFileName)) if __name__ == "__main__": unittest.main()