Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/hmmer/tests/TestLaunchPreProcessHmmpfamPostProcessNotInParallel.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 commons.pyRepetUnit.hmmer.LaunchPreProcessHmmpfamPostProcessNotInParallel 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/configTestLaunchPreProcessHmmpfamPostProcessNotInParallel.cfg" | |
19 CURRENT_DIR = os.getcwd() | |
20 | |
21 class TestLaunchPreProcessHmmpfamPostProcessNotInParallel(unittest.TestCase): | |
22 | |
23 def setUp( self ): | |
24 os.chdir(CURRENT_DIR) | |
25 self._LaunchPreProcessHmmpfamPostProcess = LaunchPreProcessHmmpfamPostProcessNotInParallel() | |
26 self._configFile = CONFIG_FILE | |
27 config = ConfigParser.ConfigParser() | |
28 config.readfp(open(self._configFile)) | |
29 self._InputFile = config.get("hmmer_config", "input_file") | |
30 self._OutputFile = config.get("hmmer_config", "output_file") | |
31 self.fileUtils = FileUtils() | |
32 | |
33 def testRun(self): | |
34 #Normal launch | |
35 self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile ) | |
36 self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( self._OutputFile ) | |
37 self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile ) | |
38 self._LaunchPreProcessHmmpfamPostProcess.run() | |
39 self.assertTrue(self.fileUtils.isRessourceExists(self._OutputFile)) | |
40 self.assertFalse(self.fileUtils.isFileEmpty(self._OutputFile)) | |
41 os.system("rm " + self._OutputFile) | |
42 #without config file | |
43 configFile = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/configdummy.cfg" | |
44 self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( configFile ) | |
45 self._LaunchPreProcessHmmpfamPostProcess.run() | |
46 self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) | |
47 #without input file | |
48 InputFile = "" | |
49 self._LaunchPreProcessHmmpfamPostProcess.setInputFile( InputFile ) | |
50 self._LaunchPreProcessHmmpfamPostProcess.run() | |
51 self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) | |
52 #without output file | |
53 self._LaunchPreProcessHmmpfamPostProcess.setConfigFile( self._configFile ) | |
54 self._LaunchPreProcessHmmpfamPostProcess.setInputFile( self._InputFile ) | |
55 OutputFile = "" | |
56 self._LaunchPreProcessHmmpfamPostProcess.setOutputFile( OutputFile ) | |
57 self._LaunchPreProcessHmmpfamPostProcess.run() | |
58 self.assertFalse(self.fileUtils.isRessourceExists(self._OutputFile)) | |
59 | |
60 | |
61 | |
62 if __name__ == "__main__": | |
63 unittest.main() |