--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateAfastaFileInAllFrameAndReplaceStopsByX.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,80 @@
+import os
+import unittest
+from commons.core.utils.FileUtils import FileUtils
+
+class Test_TranslateAfastaFileInAllFrameAndReplaceStopsByX(unittest.TestCase):
+    
+    def setUp(self):
+        self._inputFile = "dummyInputFile"
+        self._outputFile = "dummyOuputFile"
+        self._prg = "translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
+        
+        
+    def testTranslateAfastaFileInAllFrameAndReplaceStopsByX_script(self):
+        f = open(self._inputFile, "w")
+        f.write(">header1 description\n")
+        f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n")
+        f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n")
+        f.write(">header2\n")
+        f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n")
+        f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA")
+        f.close()
+        # expected fasta translated file
+        f = open("expectedTranslated.fa", "w")
+        f.write(">header1_1 description\n")
+        f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n")
+        f.write(">header1_2 description\n")
+        f.write("VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL\n")
+        f.write(">header1_3 description\n")
+        f.write("WLLVDQFMITMISRRCLVAPTNQQYNASRAX\n")
+        f.write(">header1_4 description\n")
+        f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n")
+        f.write(">header1_5 description\n")
+        f.write("QALLALYCXLVGATRHLREIIVIINXSTRSH\n")
+        f.write(">header1_6 description\n")
+        f.write("KLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT\n")
+        f.write(">header2_1\n")
+        f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n")
+        f.write(">header2_2\n")
+        f.write("VASSXSVYDHNDFTXVSRGYDXSTIXCEXSL\n")
+        f.write(">header2_3\n")
+        f.write("WLLVDQFMITMISRRCLVATTNQQYNASRAX\n")
+        f.write(">header2_4\n")
+        f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n")
+        f.write(">header2_5\n")
+        f.write("QALLALYCXLVVATRHLREIIVIINXSTRSH\n")
+        f.write(">header2_6\n")
+        f.write("KLYSHYIVDXSXPRDTYVKSLXSXTDQLEAT\n")
+        f.close()
+         
+        #normal launch
+        cmd = self._prg
+        cmd += " -i %s" % ( self._inputFile )
+        cmd += " -o %s" % ( self._outputFile )
+        os.system( cmd )        
+        self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa"))
+        os.system( "rm " + self._outputFile )
+        
+        #verbose option
+        cmd = self._prg
+        cmd += " -i %s" % ( self._inputFile )
+        cmd += " -o %s" % ( self._outputFile )
+        cmd += " -v 1"
+        os.system( cmd )        
+        self.assertTrue(FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa"))
+        os.system( "rm " + self._outputFile )
+        
+        #clean option
+        cmd = self._prg
+        cmd += " -i %s" % ( self._inputFile )
+        cmd += " -o %s" % ( self._outputFile )
+        cmd += " -c"
+        os.system( cmd )        
+        self.assertTrue( FileUtils.are2FilesIdentical( self._outputFile, "expectedTranslated.fa" ) )
+        self.assertFalse( FileUtils.isRessourceExists( self._inputFile ) )
+        os.system( "rm " + self._outputFile)
+        os.system("rm expectedTranslated.fa")
+        
+        
+if __name__ == "__main__":                 
+    unittest.main()
\ No newline at end of file