--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_clusterizeBySlidingWindows.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,79 @@
+import unittest
+import os
+from commons.core.utils.FileUtils import FileUtils
+from SMART.Java.Python.misc import Utils
+
+
+class Test_F_clusterizeBySlidingWindows(unittest.TestCase):
+
+    def setUp(self):
+        self._outputFileName         = 'output.gff3'
+        self._outputCsvFileName      = 'output.csv'
+        self._outputPngFileName      = 'output.png'
+        self._expectedOutputFileName = 'expOut.png'
+        
+    def tearDown(self):
+        for fileName in (self._outputFileName, self._outputCsvFileName, self._outputPngFileName, self._expectedOutputFileName):
+            if os.path.exists(fileName):
+                os.remove(fileName)
+        
+    def test_run_default_option(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -v 0" % (self._outputFileName)
+        os.system(cmd)
+        exp = '../TestFiles/clusterize_default_expected.gff3' 
+        self.assertTrue(Utils.diff(exp, self._outputFileName))
+        
+    def test_run_default_option_map_output(self):
+        self._outputFileName         = 'output.map'
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -u map -v 0" % (self._outputFileName)
+        os.system(cmd)
+        exp = '../TestFiles/clusterize_default_expected.map' 
+        self.assertTrue(Utils.diff(exp, self._outputFileName))
+        
+    def test_run_newTag_option(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -w newTag -v 0" % (self._outputFileName)
+        os.system(cmd)
+        exp = '../TestFiles/clusterize_output_tag_expected.gff3' 
+        self.assertTrue(Utils.diff(exp, self._outputFileName))
+        
+    def test_run_normalize_option(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -m -v 0" % (self._outputFileName)
+        os.system(cmd)
+        exp = '../TestFiles/clusterize_normalize_expected.gff3' 
+        self.assertTrue(Utils.diff(exp, self._outputFileName))
+
+    def test_run_strand_option(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -2 -v 0"  % (self._outputFileName)
+        os.system(cmd)
+        exp = '../TestFiles/clusterize_strands_expected.gff3'
+        self.assertTrue(Utils.diff(exp, self._outputFileName))
+
+    def test_run_excel_option(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -x %s -v 0" % (self._outputFileName, self._outputCsvFileName)
+        os.system(cmd)
+        self.assertTrue(FileUtils.isRessourceExists(self._outputCsvFileName))
+        
+        
+    def test_run_normalize_strand_excel_option(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -m -2 -x %s -v 0" % (self._outputFileName, self._outputCsvFileName)
+        os.system(cmd)
+        self.assertTrue(FileUtils.isRessourceExists(self._outputCsvFileName))
+      
+    def test_run_tag_operation_options(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/testSW.gff3 -f gff -s 100 -e 0 -g value1 -r min -o %s -v 0" % (self._outputFileName)
+        os.system(cmd)
+        exp = open(self._expectedOutputFileName, 'w')
+        exp.write("chr1\tS-MART\ttranscript\t1\t100\t.\t+\t.\tnbElements=0;minValue1=0;ID=region1;Name=region1\n")
+        exp.write("chr1\tS-MART\ttranscript\t101\t200\t.\t+\t.\tnbElements=2.000000;minValue1=1.0;ID=region2;Name=region2\n")
+        exp.write("chr1\tS-MART\ttranscript\t201\t300\t.\t+\t.\tnbElements=2.000000;minValue1=10.0;ID=region3;Name=region3\n")
+        exp.close()   
+        self.assertTrue(Utils.diff(self._outputFileName, self._expectedOutputFileName))
+        
+    def test_run_plot_options(self):
+        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/testSW.gff3 -f gff -s 100 -e 0 -g value1 -r min -o %s -p %s -v 0" % (self._outputFileName, self._outputPngFileName)
+        os.system(cmd)     
+        self.assertTrue(FileUtils.isRessourceExists(self._outputPngFileName))
+        
+        
+if __name__ == "__main__":
+    unittest.main()