--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_F_LaunchRefAlign.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,72 @@
+import unittest
+import os
+from commons.core.utils.FileUtils import FileUtils
+from commons.launcher.LaunchRefAlign import LaunchRefAlign
+
+
+class Test_F_LaunchRefAlign(unittest.TestCase):
+    
+    def setUp(self):
+        self._inputFastaFileName = "input.fa"
+        self._obsOutputFileName = "obs"
+        self._expOutputFileName = "exp"
+        self._writeInputFile()
+        self._writeExpOutputFile()
+        
+#    def tearDown(self):
+#        try:
+#            os.remove(self._inputFastaFileName)
+#        except:pass
+#    
+#        try:
+#            os.remove(self._expOutputFileName)
+#        except:pass
+#        try:
+#            os.remove(self._obsOutputFileName)
+#        except:pass
+#        try:
+#            os.remove("input.fa.2.3.5.80.10.20.15.dat")
+#        except:pass
+    
+    def test_run(self):
+        ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5)
+        ilauncher.run()
+        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
+        
+#    def test_run_as_script(self):
+#        cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName)
+#        os.system(cmd)
+#        self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))    
+
+        
+    def _writeInputFile(self):        
+        InputFile = open(self._inputFastaFileName, 'w')
+        InputFile.write('>sequence\n')
+        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
+        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
+        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
+        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
+        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
+        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
+        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
+        InputFile.write('>sequence2\n')
+        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
+        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
+        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
+        InputFile.close()    
+        
+    def _writeExpOutputFile(self):
+        with open(self._expOutputFileName,'w') as expOutputFile:
+            expOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21
+2\t(GGT)5\tsequence\t10\t23
+3\t(GTGTGA)4\tsequence\t222\t242
+4\t(GTCCA)2\tsequence\t282\t292
+5\t(AGTG)4\tsequence\t355\t371
+6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152
+7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151
+8\t(TC)23\tsequence2\t107\t152
+""")
+
+                       
+if __name__ == "__main__":
+    unittest.main()
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