Mercurial > repos > yufei-luo > s_mart
view 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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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()