--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_getLetterDistribution.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,118 @@
+import os
+import sys
+import unittest
+from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFasta
+from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFastq
+from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionExpectedCSV
+
+class Test_F_getLetterDistribution(unittest.TestCase):
+	
+	def tearDown(self):
+		os.system("rm tmp*.*")
+
+	def test_getLetterDistributionWithFasta(self):
+		iFastaMock = MockGetLetterDistributionFasta()
+		fastaFileName = "MockFasta_GetLetterDistribution.fa"
+		iFastaMock.write(fastaFileName)
+
+		outputName = "dummy_result_fasta"		
+		os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s" % (os.environ["REPET_PATH"], fastaFileName, outputName))
+
+		self.assertTrue (os.path.exists(outputName + ".png"))
+		self.assertTrue (os.path.exists(outputName + "PerNt.png"))
+
+		os.remove(outputName + ".png")
+		os.remove(outputName + "PerNt.png")
+		os.remove(fastaFileName)
+
+	def test_getLetterDistributionWithFastq(self):
+		iFastqMock = MockGetLetterDistributionFastq()
+		fastqFileName = "MockFastq_GetLetterDistribution.fastq"
+		iFastqMock.write(fastqFileName)
+
+		outputName = "dummy_result_fastq"		
+		os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s" % (os.environ["REPET_PATH"], fastqFileName, outputName))
+
+		self.assertTrue (os.path.exists(outputName + ".png"))
+		self.assertTrue (os.path.exists(outputName + "PerNt.png"))
+
+		os.remove(fastqFileName)
+		os.remove(outputName + ".png")
+		os.remove(outputName + "PerNt.png")
+
+	def test_getLetterDistributionWithFastaCSVOutput(self):
+		iFastaMock = MockGetLetterDistributionFasta()
+		fastaFileName = "MockFasta_GetLetterDistribution.fa"
+		iFastaMock.write(fastaFileName)
+
+		iCSVMock = MockGetLetterDistributionExpectedCSV()
+		expCSVFileName = "expCSV.csv"
+		iCSVMock.write(expCSVFileName)	
+
+		outputName = "dummy_result_fasta"		
+		os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s -c" % (os.environ["REPET_PATH"], fastaFileName, outputName))
+
+		obsCSVFileName = outputName + ".csv"
+
+		self.assertTrue (os.path.exists(outputName + ".png"))
+		self.assertTrue (os.path.exists(outputName + "PerNt.png"))
+		self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
+
+		os.remove(outputName + ".png")
+		os.remove(outputName + "PerNt.png")
+		os.remove(fastaFileName)
+		os.remove(expCSVFileName)
+		os.remove(obsCSVFileName)
+	
+	def test_getLetterDistributionWithFastqCVSOutput(self):
+		iFastqMock = MockGetLetterDistributionFastq()
+		fastqFileName = "MockFastq_GetLetterDistribution.fastq"
+		iFastqMock.write(fastqFileName)
+
+		iCSVMock = MockGetLetterDistributionExpectedCSV()
+		expCSVFileName = "expCSV.csv"
+		iCSVMock.write(expCSVFileName)	
+
+		outputName = "dummy_result_fastq"		
+		os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s -c" % (os.environ["REPET_PATH"], fastqFileName, outputName))
+
+		obsCSVFileName = outputName + ".csv"
+
+		self.assertTrue (os.path.exists(outputName + ".png"))
+		self.assertTrue (os.path.exists(outputName + "PerNt.png"))
+		self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
+
+		os.remove(fastqFileName)
+		os.remove(outputName + ".png")
+		os.remove(outputName + "PerNt.png")
+		os.remove(expCSVFileName)
+		os.remove(obsCSVFileName)
+
+	def _are2FilesIdentical(self, file1, file2 ):
+		tmpFile = "diff_%s_%s" % ( os.path.basename(file1), os.path.basename(file2) )
+		cmd = "diff %s %s >> %s" % ( file1, file2, tmpFile )
+		returnStatus = os.system( cmd )
+		if returnStatus != 0:
+			msg = "ERROR: 'diff' returned '%i'" % ( returnStatus )
+			sys.stderr.write( "%s\n" % msg )
+			sys.stderr.flush()
+			os.remove( tmpFile )
+			return False
+		if self.isEmpty( tmpFile ):
+			os.remove( tmpFile )
+			return True
+		else:
+			os.remove( tmpFile )
+			return False
+
+	def getNbLinesInSingleFile(self, fileName):
+		fileHandler = open(fileName, "r" )
+		lines = fileHandler.readlines()
+		fileHandler.close()
+		return len(lines)
+
+	def isEmpty(self, fileName):
+		return 0 == self.getNbLinesInSingleFile( fileName )
+
+if __name__ == "__main__":
+	unittest.main()