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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/tests/TestProgramLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,65 @@
+import os
+import unittest
+from pyRepet.launcher.programLauncher import *
+from pyRepet.util.file.FileUtils import *
+import ConfigParser 
+
+if (not os.environ.has_key("REPET_PATH")):
+    print "*** Error: no environment variable REPET_PATH"
+    exit =1 
+          
+if (not os.environ.has_key("PYTHONPATH")):
+    print "*** Error: no environment variable PYTHONPATH"
+    exit =1
+    
+if (exit == 1):    
+    sys.exit(1)
+
+CONFIG_FILE = "datas/config.cfg"
+CURRENT_DIR = os.getcwd()
+
+class TestProgramLauncher(unittest.TestCase):
+  
+    def setUp(self):
+        os.chdir(CURRENT_DIR)
+        self._programLauncherInstance = programLauncher()
+        self._configFile = CONFIG_FILE
+        config = ConfigParser.ConfigParser()
+        config.readfp( open(self._configFile) )
+        self._configFile = CONFIG_FILE
+        config = ConfigParser.ConfigParser()
+        config.readfp(open(self._configFile))
+        self._inputFile = config.get("hmmer_config", "input_file")
+        self._outputFile = config.get("hmmer_config", "output_file")
+        self.fileUtils = FileUtils()
+    
+    def testLaunchHmmpfam(self):
+        config = ConfigParser.ConfigParser()
+        config.readfp( open(self._configFile) )
+        self._programLauncherInstance.reset( self._inputFile )
+        self._programLauncherInstance.setOutputFileName( self._outputFile )
+        self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
+                              inputFormat=config.get("profil_search","InputFormat"),
+                              profilDatabank=config.get("profil_search","ProfilDatabank"))        
+        self.assertTrue(self.fileUtils.isRessourceExists(self._outputFile))  
+        self.assertFalse(self.fileUtils.isFileEmpty(self._outputFile))        
+        os.system( "rm " + self._outputFile)
+        self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa2.fa"
+        self._programLauncherInstance.reset( self._inputFile )
+        self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
+                              inputFormat=config.get("profil_search","InputFormat"),
+                              profilDatabank=config.get("profil_search","ProfilDatabank"))
+        self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
+        #No output file
+        self._outputFile = ""
+        self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa.fa"
+        self._programLauncherInstance.reset( self._inputFile )
+        self._programLauncherInstance.setOutputFileName( self._outputFile )
+        self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
+                              inputFormat=config.get("profil_search","InputFormat"),
+                              profilDatabank=config.get("profil_search","ProfilDatabank"))
+        self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
+        os.chdir(CURRENT_DIR)
+    
+if __name__ == "__main__":                 
+    unittest.main()