comparison commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamAndParse2alignLauncherInParallel.py @ 18:94ab73e8a190

Uploaded

18:94ab73e8a190

import os
import sys
import unittest
from sets import Set
import ConfigParser 
from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher
from pyRepet.sql.RepetJobMySQL import *
from pyRepet.util.file.FileUtils import *

CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg"
CURRENT_DIR = os.getcwd()

class TestFunctionalHmmpfamLauncherAndParse2alignInparallel(unittest.TestCase):
    
    def setUp(self):
        self._config = ConfigParser.ConfigParser()
        self._config.readfp( open(CONFIG_FILE) )
        os.chdir(CURRENT_DIR)

    def testHmmpfamAndParse2alignHasRunInparallel (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)
        params = {"param":"--informat FASTA -E 10", 
                  "profilDB": self._config.get("profil_search", "ProfilDatabank"), 
                  "outputDir": self._config.get("hmmer_config", "result_dir"),
                  "query": self._config.get("hmmer_config", "query_dir"),
                  "job_table":"jobs", 
                  "queue" : self._config.get("sge_config", "queue"), 
                  "groupid" : self._config.get("sge_config", "groupid"),
                  "tmpDir": self._config.get("hmmer_config", "tmp_dir"),
                  "scriptToLaunch": self._config.get("parse_config", "scriptToLaunch"),
                  "cDir" : "."}
        self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params)
        self.hmmpfamAndParse2align.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.align", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut.align"])
        self.assertTrue( alignFileSet.issubset(dirSet))
        self._clean()

    def _clean(self):
        
        dirToClean = self._config.get( "hmmer_config", "tmp_dir" )
        os.system("rm  " + dirToClean + "/*")
        dirToClean = self._config.get( "hmmer_config", "result_dir" )
        os.system("rm  " + dirToClean + "/*")
        os.system("rm  HmmpfamJob*.e*")
        os.system("rm  HmmpfamJob*.o*")


if __name__ == "__main__":
        unittest.main()