diff commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmpfamOutputProcessing.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmpfamOutputProcessing.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,58 @@
+import os
+import unittest
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
+from commons.core.utils.FileUtils import FileUtils
+
+class TestHmmpfamOutputProcessing(unittest.TestCase):
+    
+    def setUp(self):
+        self.fileUtils = FileUtils()
+        self.hmmpfamOutputProcess = HmmpfamOutputProcessing()
+        self._inputFile = "./datas/Outputhmmpfam" 
+        self._inputFile2 = "./datas/test_hmmpfam_output"
+        self._outputFile = "./datas/dummyAlignFile.align"
+        
+    def testReadHmmOutput(self):
+        file = open( self._inputFile )
+        pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file)
+        self.assertEqual(["7LES_DROME", "437", "522", "fn3", "1", "84", "8.8e-15", "48.3"], pfamOutput.get(0))
+        self.assertEqual(["7LES_DROME", "825", "914", "fn3", "1", "84", "2.2e-06", "13.4"], pfamOutput.get(1))
+        self.assertEqual(["7LES_DROME", "1292", "1389", "fn3", "1", "84", "1.2e-06", "15.9"], pfamOutput.get(2))
+        self.assertEqual(["7LES_DROME", "1799", "1891", "fn3", "1", "84", "2.3e-19", "63.5"], pfamOutput.get(3))
+        self.assertEqual(["7LES_DROME", "1899", "1978", "fn3", "1", "84", "1.5e-06", "15.2"], pfamOutput.get(4))
+        self.assertEqual(["7LES_DROME", "1993", "2107", "fn3", "1", "84", "4.3e-07", "20.3"], pfamOutput.get(5))
+        self.assertEqual(["7LES_DROME", "2209", "2483", "pkinase", "1", "294", "6e-95", "314.6"], pfamOutput.get(6))
+        self.assertEqual(["7LES_DROME", "2223", "2284", "rrm", "1", "77", "0.72", "-40.4"], pfamOutput.get(7))
+        file.close()
+        
+    def test_readHmmOutput_empty_file(self):
+        file = open( "./datas/OutputhmmpfamEmpty", "w" )
+        file.close()
+        file = open( "./datas/OutputhmmpfamEmpty")
+        pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file)
+        file.close()
+        self.assertEqual(None, pfamOutput)
+        os.system("rm ./datas/OutputhmmpfamEmpty")
+        
+    def testParseHmmpfamOutput2Align(self):
+        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile2, self._outputFile)
+        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
+        self.assertEqual(18, FileUtils.getNbLinesInSingleFile(self._outputFile))
+        os.system("rm " + self._outputFile)
+        
+    def test_parseHmmpfamOutput2Align_empty_file(self):
+        file = open("./datas/dummy_hmmpfam_output", "w")
+        file.close()
+        self._inputFile = "./datas/dummy_hmmpfam_output"
+        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
+        self.assertTrue(FileUtils.isEmpty(self._outputFile))
+        os.system("rm " + self._inputFile)
+        os.system("rm " + self._outputFile)
+        
+    def test_parseHmmpfamOutput2Align_file_not_exists(self):
+        self._inputFile = "./datas/dummy_hmmpfam_output"
+        self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile )
+        self.assertFalse(FileUtils.isRessourceExists(self._outputFile))
+        
+if __name__ == "__main__":                 
+    unittest.main()
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