Mercurial > repos > yufei-luo > s_mart
comparison 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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17:b0e8584489e6 | 18:94ab73e8a190 |
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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() |