Mercurial > repos > yufei-luo > s_mart
view commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.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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import os import sys import unittest from sets import Set import ConfigParser from pyRepet.sql.RepetJobMySQL import * from pyRepet.util.file.FileUtils import * import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg" CURRENT_DIR = os.getcwd() class TestFunctionalHmmpfamClusterComponent(unittest.TestCase): def setUp(self): os.chdir(CURRENT_DIR) self._config = ConfigParser.ConfigParser() self._config.readfp( open(CONFIG_FILE) ) self._hmmer = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent() def testHmmpfamHasRunInparallel (self): user = self._config.get( "db_config","user" ) host = self._config.get( "db_config","host" ) passwd = self._config.get( "db_config","passwd" ) dbName = self._config.get( "db_config","dbname" ) jobDb = RepetJob(user , host , passwd , dbName) self._hmmer.setJobDb(jobDb) self._hmmer.loadConfig(self._config) self._hmmer.run() fileUtils = FileUtils() dirFiles = fileUtils.listDir(self._config.get("hmmer_config", "result_dir")) dirSet = Set(dirFiles) alignFileSet = Set([self._config.get("hmmer_config", "result_dir") + "/" + "batch_1.fa.hmmpfamOut", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut"]) self.assertTrue(alignFileSet.issubset(dirSet)) self._hmmer.clean() if __name__ == "__main__": unittest.main()