Mercurial > repos > yufei-luo > s_mart
diff commons/pyRepetUnit/hmmer/tests/TestProgramLauncher.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /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()