Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
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()