--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmOutputProcessing.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,36 @@
+import os
+import unittest
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing
+from commons.core.utils.FileUtils import FileUtils
+
+class TestHmmOutputProcessing(unittest.TestCase):
+    
+    def setUp(self):
+        self.hmmOutput = HmmOutputProcessing()
+        self._inputFile = "./datas/test_hmmpfam_output" 
+        self._outputFile =  "./datas/dummyoutput.align" 
+        self._inputFileScan2 = "./datas/hmmscanOutput"
+        self._outputFileScan2 = "./datas/hmmscanOutput.align"       
+        
+    def test_writeHmmOutputToAlignFile(self):
+        output = open("./datas/output.align", "w")
+        output.write("SAR:satellite:satellite_5\t3\t9\tDUF751\t5\t11\t5.4\t5.4\t0\n")
+        output.write("SAR:satellite:satellite_5\t17\t23\tDUF751\t5\t11\t5.1\t5.5\t0\n")
+        output.write("SAR:satellite:satellite_5\t3\t21\tClenterotox\t173\t191\t0.66\t7.4\t0\n")
+        output.close()
+        pfamOutput = HmmOutput()
+        pfamOutput.append(["SAR:satellite:satellite_5", "3", "9", "DUF751", "5", "11", "5.4", "5.4"])
+        pfamOutput.append(["SAR:satellite:satellite_5", "17", "23", "DUF751", "5", "11", "5.1", "5.5"])
+        pfamOutput.append(["SAR:satellite:satellite_5", "3", "21", "Clenterotox", "173", "191", "0.66", "7.4"])
+        fout = open("./datas/outputGen.align", "w")
+        self.hmmOutput.writeHmmOutputToAlignFile(pfamOutput, fout)
+        fout.close()
+        self.assertTrue(FileUtils.are2FilesIdentical("./datas/output.align", "./datas/outputGen.align"))
+        os.remove("./datas/output.align")
+        os.remove("./datas/outputGen.align")
+        
+if __name__ == "__main__":                 
+    unittest.main()
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