Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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30:5677346472b5 | 31:0ab839023fe4 |
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1 import os | |
2 import sys | |
3 import unittest | |
4 from sets import Set | |
5 import ConfigParser | |
6 from pyRepet.sql.RepetJobMySQL import * | |
7 from pyRepet.util.file.FileUtils import * | |
8 import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent | |
9 | |
10 CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg" | |
11 CURRENT_DIR = os.getcwd() | |
12 | |
13 class TestFunctionalHmmpfamClusterComponent(unittest.TestCase): | |
14 | |
15 def setUp(self): | |
16 os.chdir(CURRENT_DIR) | |
17 self._config = ConfigParser.ConfigParser() | |
18 self._config.readfp( open(CONFIG_FILE) ) | |
19 self._hmmer = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent() | |
20 | |
21 def testHmmpfamHasRunInparallel (self): | |
22 user = self._config.get( "db_config","user" ) | |
23 host = self._config.get( "db_config","host" ) | |
24 passwd = self._config.get( "db_config","passwd" ) | |
25 dbName = self._config.get( "db_config","dbname" ) | |
26 jobDb = RepetJob(user , host , passwd , dbName) | |
27 self._hmmer.setJobDb(jobDb) | |
28 self._hmmer.loadConfig(self._config) | |
29 self._hmmer.run() | |
30 fileUtils = FileUtils() | |
31 dirFiles = fileUtils.listDir(self._config.get("hmmer_config", "result_dir")) | |
32 dirSet = Set(dirFiles) | |
33 alignFileSet = Set([self._config.get("hmmer_config", "result_dir") + "/" + "batch_1.fa.hmmpfamOut", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut"]) | |
34 self.assertTrue(alignFileSet.issubset(dirSet)) | |
35 self._hmmer.clean() | |
36 | |
37 if __name__ == "__main__": | |
38 unittest.main() |