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1 import os
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2 import unittest
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3 from pyRepet.launcher.programLauncher import *
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4 from pyRepet.util.file.FileUtils import *
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5 import ConfigParser
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6
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7 if (not os.environ.has_key("REPET_PATH")):
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8 print "*** Error: no environment variable REPET_PATH"
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9 exit =1
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10
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11 if (not os.environ.has_key("PYTHONPATH")):
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12 print "*** Error: no environment variable PYTHONPATH"
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13 exit =1
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14
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15 if (exit == 1):
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16 sys.exit(1)
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17
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18 CONFIG_FILE = "datas/config.cfg"
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19 CURRENT_DIR = os.getcwd()
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20
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21 class TestProgramLauncher(unittest.TestCase):
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22
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23 def setUp(self):
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24 os.chdir(CURRENT_DIR)
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25 self._programLauncherInstance = programLauncher()
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26 self._configFile = CONFIG_FILE
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27 config = ConfigParser.ConfigParser()
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28 config.readfp( open(self._configFile) )
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29 self._configFile = CONFIG_FILE
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30 config = ConfigParser.ConfigParser()
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31 config.readfp(open(self._configFile))
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32 self._inputFile = config.get("hmmer_config", "input_file")
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33 self._outputFile = config.get("hmmer_config", "output_file")
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34 self.fileUtils = FileUtils()
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35
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36 def testLaunchHmmpfam(self):
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37 config = ConfigParser.ConfigParser()
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38 config.readfp( open(self._configFile) )
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39 self._programLauncherInstance.reset( self._inputFile )
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40 self._programLauncherInstance.setOutputFileName( self._outputFile )
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41 self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
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42 inputFormat=config.get("profil_search","InputFormat"),
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43 profilDatabank=config.get("profil_search","ProfilDatabank"))
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44 self.assertTrue(self.fileUtils.isRessourceExists(self._outputFile))
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45 self.assertFalse(self.fileUtils.isFileEmpty(self._outputFile))
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46 os.system( "rm " + self._outputFile)
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47 self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa2.fa"
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48 self._programLauncherInstance.reset( self._inputFile )
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49 self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
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50 inputFormat=config.get("profil_search","InputFormat"),
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51 profilDatabank=config.get("profil_search","ProfilDatabank"))
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52 self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
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53 #No output file
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54 self._outputFile = ""
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55 self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa.fa"
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56 self._programLauncherInstance.reset( self._inputFile )
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57 self._programLauncherInstance.setOutputFileName( self._outputFile )
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58 self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
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59 inputFormat=config.get("profil_search","InputFormat"),
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60 profilDatabank=config.get("profil_search","ProfilDatabank"))
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61 self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
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62 os.chdir(CURRENT_DIR)
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63
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64 if __name__ == "__main__":
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65 unittest.main()
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