diff commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateInAllFramesAndReplaceStopByX.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateInAllFramesAndReplaceStopByX.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,65 @@
+import os
+import unittest
+from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX
+from commons.core.seq.Bioseq import Bioseq
+from commons.core.utils.FileUtils import FileUtils
+
+class Test_TranslateInAllFramesAndReplaceStopByX(unittest.TestCase):
+    
+    def setUp(self):
+        self.bioseq = Bioseq()
+        self.preProcess = TranslateInAllFramesAndReplaceStopByX()
+        self._inputFile = "./datas/dummy.fa" 
+        self._outputFile =  "./datas/dummyoutput.fa" 
+        
+        
+    def testRun(self):
+        self.preProcess.setInputFile(self._inputFile)
+        self.preProcess.setOutputFile(self._outputFile)
+        # real fasta file
+        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("./datas/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()
+        self.preProcess.run()
+        self.assertTrue(FileUtils.are2FilesIdentical("./datas/expectedTranslated.fa", self._outputFile))
+        os.system("rm " + self._inputFile)
+        os.system("rm " + self._outputFile)
+        os.system("rm ./datas/expectedTranslated.fa")
+        # empty fasta file
+        #self.preProcess.translateAfastaFileInAllFrame()
+        #self.assertFalse(FileUtils.isRessourceExists(self._outputFile))
+
+if __name__ == "__main__":                 
+    unittest.main()
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