--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/tests/Test_GetMultAlignAndPhylogenyPerTErefSeq.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,54 @@
+import unittest
+import os
+import time
+from commons.core.sql.DbMySql import DbMySql
+from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
+from commons.core.utils.FileUtils import FileUtils
+
+
+class Test_GetMultAlignAndPhylogenyPerTErefSeq( unittest.TestCase ):
+    
+    def setUp( self ):
+        self.fileUtils = FileUtils()
+        self._inputTEFile = "dummyTE"
+        self._iGMAP = GetMultAlignAndPhylogenyPerTErefSeq()
+        self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
+        self._configFileName = "dummyConfig_%s" % self._uniqId
+        configFile = open( self._configFileName, "w" )
+        configFile.write("[repet_env]\n")
+        configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
+        configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
+        configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
+        configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
+        configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
+        configFile.close()
+        
+    def tearDown( self ):
+        os.remove( self._configFileName )
+        os.remove( self._inputTEFile )
+    
+        
+    def test_getNamesOfTErefSeq_fromFile_ok(self):
+        expTEList =["DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed",
+                    "DT-comp_DmelChr4-B-P0.0-Map3", "RLX-incomp_Blc3_DmelChr4-L-B3-Map1"]
+        self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
+        self.writeInputTEFile()
+        obsTEList = self._iGMAP.getNamesOfTErefSeq()
+        self.assertEqual(obsTEList, expTEList)
+    
+    def test_getNamesOfTErefSeq_from_empty_file(self):
+        expTEList =[]
+        self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
+        with open(self._inputTEFile,"w") as TEFile:
+            TEFile.write("")
+        obsTEList = self._iGMAP.getNamesOfTErefSeq()
+        self.assertEqual(obsTEList, expTEList)
+        
+    def writeInputTEFile(self):
+        with open(self._inputTEFile,"w") as TEFile:
+            TEFile.write("""DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed
+RLX-incomp_Blc3_DmelChr4-L-B3-Map1\t reverse
+DT-comp_DmelChr4-B-P0.0-Map3\t""")
+            
+if __name__ == "__main__":
+        unittest.main()
\ No newline at end of file