--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_GetDifferentialExpression.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,50 @@
+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()
+