Mercurial > repos > yufei-luo > s_mart

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

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import os
2 import unittest
3 from pyRepet.launcher.programLauncher import *
4 from pyRepet.util.file.FileUtils import *
5 import ConfigParser
6
7 if (not os.environ.has_key("REPET_PATH")):
8 print "*** Error: no environment variable REPET_PATH"
9 exit =1
10
11 if (not os.environ.has_key("PYTHONPATH")):
12 print "*** Error: no environment variable PYTHONPATH"
13 exit =1
14
15 if (exit == 1):
16 sys.exit(1)
17
18 CONFIG_FILE = "datas/config.cfg"
19 CURRENT_DIR = os.getcwd()
20
21 class TestProgramLauncher(unittest.TestCase):
22
23 def setUp(self):
24 os.chdir(CURRENT_DIR)
25 self._programLauncherInstance = programLauncher()
26 self._configFile = CONFIG_FILE
27 config = ConfigParser.ConfigParser()
28 config.readfp( open(self._configFile) )
29 self._configFile = CONFIG_FILE
30 config = ConfigParser.ConfigParser()
31 config.readfp(open(self._configFile))
32 self._inputFile = config.get("hmmer_config", "input_file")
33 self._outputFile = config.get("hmmer_config", "output_file")
34 self.fileUtils = FileUtils()
35
36 def testLaunchHmmpfam(self):
37 config = ConfigParser.ConfigParser()
38 config.readfp( open(self._configFile) )
39 self._programLauncherInstance.reset( self._inputFile )
40 self._programLauncherInstance.setOutputFileName( self._outputFile )
41 self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
42 inputFormat=config.get("profil_search","InputFormat"),
43 profilDatabank=config.get("profil_search","ProfilDatabank"))
44 self.assertTrue(self.fileUtils.isRessourceExists(self._outputFile))
45 self.assertFalse(self.fileUtils.isFileEmpty(self._outputFile))
46 os.system( "rm " + self._outputFile)
47 self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa2.fa"
48 self._programLauncherInstance.reset( self._inputFile )
49 self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
50 inputFormat=config.get("profil_search","InputFormat"),
51 profilDatabank=config.get("profil_search","ProfilDatabank"))
52 self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
53 #No output file
54 self._outputFile = ""
55 self._inputFile = "repet_pipe/pyRepet/launcher/datas/hmmpfam/test_input_aa.fa"
56 self._programLauncherInstance.reset( self._inputFile )
57 self._programLauncherInstance.setOutputFileName( self._outputFile )
58 self._programLauncherInstance.launchHmmpfam( evalFilter=config.get("profil_search","Evalue"),
59 inputFormat=config.get("profil_search","InputFormat"),
60 profilDatabank=config.get("profil_search","ProfilDatabank"))
61 self.assertFalse(self.fileUtils.isRessourceExists(self._outputFile))
62 os.chdir(CURRENT_DIR)
63
64 if __name__ == "__main__":
65 unittest.main()