view smart_toolShed/commons/core/checker/test/Test_CheckerUtils.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
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# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info". 
#
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# modify and redistribute granted by the license, users are provided only
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# economic rights,  and the successive licensors  have only  limited
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# In this respect, the user's attention is drawn to the risks associated
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import unittest
import os
import ConfigParser
from commons.core.checker.CheckerUtils import CheckerUtils
from commons.core.checker.CheckerException import CheckerException
from ConfigParser import NoOptionError
from ConfigParser import NoSectionError

class Test_CheckerUtils( unittest.TestCase ):
    
    def setUp(self):
        self.queueFileName = "queueName.txt"
        self.configFileName = "dummyConfig.cfg"
    
    def tearDown(self):
        if os.path.exists(self.queueFileName):
            os.remove(self.queueFileName)
        if os.path.exists(self.configFileName):
            os.remove(self.configFileName)
    
    def test_isBlastNameInBlastValues( self ):
        correctValueList = [ "blastn", "blastp", "blastx", "tblastn", "tblastx" ]
        for value in correctValueList:
            self.assertFalse( CheckerUtils.isBlastNameNotInBlastValues( value ) )
            
        incorrectValueList = [ "badbalst", "wublast" ]
        for value in incorrectValueList:
            self.assertTrue( CheckerUtils.isBlastNameNotInBlastValues( value ) )
            
    def test_isNotTRUEisNotFALSE( self ):
        correctValueList = [ "TRUE", "FALSE" ]
        for value in correctValueList:
            self.assertFalse( CheckerUtils.isNotTRUEisNotFALSE( value ) )
            
        incorrectValueList = [ "True", "False" ]
        for value in incorrectValueList:
            self.assertTrue( CheckerUtils.isNotTRUEisNotFALSE( value ) )
            
    def test_isRessourceNotExists( self ):
        fileName = "dummyFile.txt"
        self.assertTrue( CheckerUtils.isRessourceNotExits( fileName ) )
        os.system( "touch %s" % ( fileName ) )
        self.assertFalse( CheckerUtils.isRessourceNotExits( fileName ) )
        os.remove( fileName )
        
    def test_isNotAeValueWithOneDigit2DecimalsAtLeast( self ):
        correctEValueList = [ "5e-32", "7e-45", "1e-2122", "9e-32" ]
        for value in correctEValueList:
            self.assertFalse( CheckerUtils.isNotAeValueWithOneDigit2DecimalsAtLeast( value ) )
            
        incorrecEValueStr = [ "10e-32", "2e-3", "2e-2", "1", "cxhhe" ]
        for value in incorrecEValueStr:
            self.assertTrue( CheckerUtils.isNotAeValueWithOneDigit2DecimalsAtLeast( value ) )
            
    def test_isNotADigit( self ):
        correctDigitList = [ "1", "21", "345" ]
        for value in correctDigitList:
            self.assertFalse( CheckerUtils.isNotANumber( value ) )
            
        incorrectDigitList = [ "A", "dfdf", "((((" ]
        for value in incorrectDigitList:
            self.assertTrue( CheckerUtils.isNotANumber( value ) )
            
    def test_isExecutableInUserPath( self ):
        exeName = "ls"
        self.assertTrue( CheckerUtils.isExecutableInUserPath( exeName ) )

        exeName = "hsvegdtefaobfbcheta"
        self.assertFalse( CheckerUtils.isExecutableInUserPath( exeName ) )
    
    def test_isExecutableInUserPath_case_endsWith( self ):
        exeName = "s"
        self.assertFalse( CheckerUtils.isExecutableInUserPath( exeName ) )

    def test_isQueueNameValid_valid(self):
        cmd = "qconf -sql > " + self.queueFileName
        os.system(cmd)
        f = open(self.queueFileName, "r")
        lQueueNames = f.readlines()
        f.close()
        if lQueueNames == []:
            print "Warning you need SGE installed\n"
        else:
            self.assertTrue(CheckerUtils.isQueueNameValid(lQueueNames[0].strip()))
        
    def test_isQueueNameValid_not_valid(self):
        cmd = "qconf -sql > " + self.queueFileName
        os.system(cmd)
        f = open(self.queueFileName, "r")
        lQueueNames = f.readlines()
        f.close()
        if lQueueNames == []:
            print "Warning you need SGE installed\n"
        else:
            self.assertFalse(CheckerUtils.isQueueNameValid("dummyQueueName"))

    def test_isQueueNameValid_valid_with_parameter(self):
        cmd = "qconf -sql > " + self.queueFileName
        os.system(cmd)
        f = open(self.queueFileName, "r")
        lQueueNames = f.readlines()
        f.close()
        if lQueueNames == []:
            print "Warning you need SGE installed\n"
        else:
            queueNameWithParameter = lQueueNames[0].strip() + " test=TRUE"
            self.assertTrue(CheckerUtils.isQueueNameValid(queueNameWithParameter))
            
    def test_isCharAlphanumOrUnderscore_valid(self):
        project_name = "Project_Name"
        self.assertTrue(CheckerUtils.isCharAlphanumOrUnderscore(project_name))
        
    def test_isCharAlphanumOrUnderscore_not_valid(self):
        project_name = "Project_Name,"
        self.assertFalse(CheckerUtils.isCharAlphanumOrUnderscore(project_name))
        
    def test_isMax15Char_valid(self):
        project_name = "Project_Name"
        self.assertTrue(CheckerUtils.isMax15Char(project_name))
        
    def test_isMax15Char_not_valid(self):
        project_name = "Project_Name_tooLong"
        self.assertFalse(CheckerUtils.isMax15Char(project_name))
        
    def test_checkSectionInConfigFile_empty_section(self):
        sectionName = "sectionName"
        line = "[" + sectionName + "]"
        configFile = open(self.configFileName, "w")
        configFile.write(line)
        configFile.close()
        configFile = open(self.configFileName, "r")
        
        config = ConfigParser.ConfigParser()
        config.readfp(configFile)
        
        isSectionExceptionRaised = False
        try:
            CheckerUtils.checkSectionInConfigFile(config, sectionName)
        except NoSectionError:
            isSectionExceptionRaised = True
        configFile.close()
        self.assertFalse(isSectionExceptionRaised)
    
    def test_checkSectionInConfigFile(self):
        sectionName = "sectionName"
        lines = "[" + sectionName + "]\ndummyOption : dummyOption\n"
        configFile = open(self.configFileName, "w")
        configFile.write(lines)
        configFile.close()
        configFile = open(self.configFileName, "r")
        
        config = ConfigParser.ConfigParser()
        config.readfp(configFile)
        
        isSectionExceptionRaised = False
        try:
            CheckerUtils.checkSectionInConfigFile(config, sectionName)
        except NoSectionError:
            isSectionExceptionRaised = True
        configFile.close()
        self.assertFalse(isSectionExceptionRaised)
        
    def test_checkSectionInConfigFile_not_valid(self):
        sectionName = "sectionName"
        line = " "
        configFile = open(self.configFileName, "w")
        configFile.write(line)
        configFile.close()
        configFile = open(self.configFileName, "r")
        
        config = ConfigParser.ConfigParser()
        config.readfp(configFile)
        
        isSectionExceptionRaised = False
        try:
            CheckerUtils.checkSectionInConfigFile(config, sectionName)
        except NoSectionError:
            isSectionExceptionRaised = True
        configFile.close()
        self.assertTrue(isSectionExceptionRaised)
        
    def test_checkOptionInSectionInConfigFile(self):
        optionName = "optionName"
        sectionName = "sectionName"
        configFile = open(self.configFileName, "w")
        configFile.write("[" + sectionName + "]\n")
        configFile.write(optionName + ": ")
        configFile.close()
        configFile = open(self.configFileName, "r")
        
        config = ConfigParser.ConfigParser()
        config.readfp(configFile)
        
        isSectionExceptionRaised = False
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(config, sectionName, optionName)
        except NoOptionError:
            isSectionExceptionRaised = True
        configFile.close()
        self.assertFalse(isSectionExceptionRaised)
        
    def test_checkOptionInSectionInConfigFile_not_present(self):
        optionName = " "
        sectionName = "sectionName"
        configFile = open(self.configFileName, "w")
        configFile.write("[" + sectionName + "]\n")
        configFile.write(optionName)
        configFile.close()
        configFile = open(self.configFileName, "r")
        
        config = ConfigParser.ConfigParser()
        config.readfp(configFile)
        
        isSectionExceptionRaised = False
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(config, sectionName, optionName)
        except NoOptionError:
            isSectionExceptionRaised = True
        configFile.close()
        self.assertTrue(isSectionExceptionRaised)
        
    def test_checkOptionInSectionInConfigFile_not_in_the_right_section(self):
        optionName = "optionName"
        rightSection = "dummySection2"
        configFile = open(self.configFileName, "w")
        configFile.write("[dummySection1]\n")
        configFile.write(optionName + ": \n")
        configFile.write("[" + rightSection + "]")
        configFile.close()
        configFile = open(self.configFileName, "r")
        
        config = ConfigParser.ConfigParser()
        config.readfp(configFile)
        
        isSectionExceptionRaised = False
        try:
            CheckerUtils.checkOptionInSectionInConfigFile(config, rightSection, optionName)
        except NoOptionError:
            isSectionExceptionRaised = True
        configFile.close()
        self.assertTrue(isSectionExceptionRaised)
        
    def test_checkConfigVersion_different_version_between_changeLog_and_configFile(self):
        changeLogFileName = "dummyCHANGELOG"
        
        self._writeChangeLogFile(changeLogFileName)
        self._writeConfigFile("repet_version: 1.3.5\n")
        
        changeLogFileHandler = open(changeLogFileName, "r")
        configFileHandler = open(self.configFileName, "r")
        config = ConfigParser.ConfigParser()
        config.readfp(configFileHandler)
        
        self.assertRaises(CheckerException, CheckerUtils.checkConfigVersion, changeLogFileHandler, config)
        
        changeLogFileHandler.close()
        configFileHandler.close()
        os.remove(changeLogFileName)
        
    def test_checkConfigVersion_same_version_between_changeLog_and_configFile(self):
        changeLogFileName = "dummyCHANGELOG"
        self._writeChangeLogFile(changeLogFileName)
        self._writeConfigFile("repet_version: 1.3.6\n")
        
        changeLogFileHandler = open(changeLogFileName, "r")
        configFileHandler = open(self.configFileName, "r")
        config = ConfigParser.ConfigParser()
        config.readfp(configFileHandler)
        
        isCheckerExceptionRaised = False
        try:
            CheckerUtils.checkConfigVersion(changeLogFileHandler, config)
        except CheckerException:
            isCheckerExceptionRaised = True
        self.assertFalse(isCheckerExceptionRaised)
        
        changeLogFileHandler.close()
        configFileHandler.close()
        os.remove(changeLogFileName)
        
    def test_getVersionFromChangelogFile(self):
        changeLogFileName = "dummyCHANGELOG"
        self._writeChangeLogFile(changeLogFileName)
        obsVer = CheckerUtils.getVersionFromChangelogFile(changeLogFileName)
        expVer = "1.3.6"
        
        self.assertEquals(obsVer, expVer)
        
        os.remove(changeLogFileName)
        
    def test_checkConfigVersion_check_exception_message(self):
        changeLogFileName = "dummyCHANGELOG"
        self._writeChangeLogFile(changeLogFileName)
        self._writeConfigFile("repet_version: 1.3.5\n")
        
        changeLogFileHandler = open(changeLogFileName, "r")
        configFileHandler = open(self.configFileName, "r")
        config = ConfigParser.ConfigParser()
        config.readfp(configFileHandler)
        
        checkerExceptionInstance = None
        try:
            CheckerUtils.checkConfigVersion(changeLogFileHandler, config)
        except CheckerException, e:
            checkerExceptionInstance = e
        
        expMessage = "*** Error: wrong config file version. Expected version num is 1.3.6 but actual in config file is 1.3.5"
        obsMessage = checkerExceptionInstance.msg
           
        self.assertEquals(expMessage, obsMessage)
        
    def test_checkHeaders_first_header_with_question_mark(self):
        fastaFileName = "dummyFasta.fa"
        self._writeFastaFile_first_header_with_question_mark(fastaFileName)
        fastaFileHandler = open(fastaFileName,"r")
        isExceptionRaised = False
        try:
            CheckerUtils.checkHeaders(fastaFileHandler)
        except CheckerException, e:
            isExceptionRaised = True
            
        fastaFileHandler.close()
        os.remove(fastaFileName)
            
        self.assertTrue(isExceptionRaised)
        
        expMessages = ["DmelChr4_Bla?ster_Piler_0.0_Map_3"] 
        obsMessages = e.getMessages()
        
        self.assertEquals(expMessages, obsMessages)

    def test_checkHeaders_with_2_wrong_headers(self):
        fastaFileName = "dummyFasta.fa"
        self._writeFastaFile_with_2_wrong_headers(fastaFileName)
        fastaFileHandler = open(fastaFileName,"r")
        isExceptionRaised = False
        try:
            CheckerUtils.checkHeaders(fastaFileHandler)
        except CheckerException, e:
            isExceptionRaised = True
            
        fastaFileHandler.close()
        os.remove(fastaFileName)
            
        self.assertTrue(isExceptionRaised)
        
        expMessages = ["DmelChr4_Bla?ster_Piler_0.0_Map_3","DmelChr4_Bla!ster_Piler_1.0_Map_9"] 
        obsMessages = e.getMessages()
        
        self.assertEquals(expMessages, obsMessages)

    def test_checkHeaders_with_pipe(self):
        fastaFileName = "dummyFasta.fa"
        self._writeFastaFile_with_pipe(fastaFileName)
        fastaFileHandler = open(fastaFileName,"r")
        isExceptionRaised = False
        try:
            CheckerUtils.checkHeaders(fastaFileHandler)
        except CheckerException, e:
            isExceptionRaised = True
            
        fastaFileHandler.close()
        os.remove(fastaFileName)
            
        self.assertTrue(isExceptionRaised)
        
        expMessages = ["DmelC|hr4_Blas-ter_Piler_1.0_Map_9"] 
        obsMessages = e.getMessages()
        
        self.assertEquals(expMessages, obsMessages)

    def test_checkHeaders_with_equal(self):
        fastaFileName = "dummyFasta.fa"
        self._writeFastaFile_with_equal(fastaFileName)
        fastaFileHandler = open(fastaFileName,"r")
        isExceptionRaised = False
        try:
            CheckerUtils.checkHeaders(fastaFileHandler)
        except CheckerException, e:
            isExceptionRaised = True
            
        fastaFileHandler.close()
        os.remove(fastaFileName)
            
        self.assertTrue(isExceptionRaised)
        
        expMessages = ["DmelC:hr4_Blas=ter_Piler_1.0_Map_9"] 
        obsMessages = e.getMessages()
        
        self.assertEquals(expMessages, obsMessages)

    def test_checkHeaders_all_headers_ok(self):
        fastaFileName = "dummyFasta.fa"
        self._writeFastaFile_all_headers_ok(fastaFileName)
        fastaFileHandler = open(fastaFileName,"r")
        isExceptionRaised = False
        try:
            CheckerUtils.checkHeaders(fastaFileHandler)
        except CheckerException:
            isExceptionRaised = True
            
        fastaFileHandler.close()
        os.remove(fastaFileName)
            
        self.assertFalse(isExceptionRaised)

    def _writeFastaFile_first_header_with_question_mark(self, fastaFileName):    
        fastaFileHandler = open(fastaFileName, "w")
        fastaFileHandler.write(">DmelChr4_Bla?ster_Piler_0.0_Map_3\n")
        fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
        fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
        fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
        fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
        fastaFileHandler.write(">DmelChr4_Blaster_Piler_1.0_Map_9\n")
        fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
        fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
        fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
        fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
        fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
        fastaFileHandler.close()
    
    def _writeFastaFile_with_2_wrong_headers(self, fastaFileName):    
        fastaFileHandler = open(fastaFileName, "w")
        fastaFileHandler.write(">DmelChr4_Bla?ster_Piler_0.0_Map_3\n")
        fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
        fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
        fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
        fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
        fastaFileHandler.write(">DmelChr4_Bla!ster_Piler_1.0_Map_9\n")
        fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
        fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
        fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
        fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
        fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
        fastaFileHandler.close()
    
    def _writeFastaFile_all_headers_ok(self, fastaFileName):    
        fastaFileHandler = open(fastaFileName, "w")
        fastaFileHandler.write(">DmelChr4_Blaster_Piler_0.0_Map_3\n")
        fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
        fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
        fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
        fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
        fastaFileHandler.write(">DmelC:hr4_Blas-ter_Piler_1.0_Map_9\n")
        fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
        fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
        fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
        fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
        fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
        fastaFileHandler.close()
    
    def _writeFastaFile_with_pipe(self, fastaFileName):    
        fastaFileHandler = open(fastaFileName, "w")
        fastaFileHandler.write(">DmelChr4_Blaster_Piler_0.0_Map_3\n")
        fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
        fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
        fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
        fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
        fastaFileHandler.write(">DmelC|hr4_Blas-ter_Piler_1.0_Map_9\n")
        fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
        fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
        fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
        fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
        fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
        fastaFileHandler.close()
    
    def _writeFastaFile_with_equal(self, fastaFileName):    
        fastaFileHandler = open(fastaFileName, "w")
        fastaFileHandler.write(">DmelChr4_Blaster_Piler_0.0_Map_3\n")
        fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
        fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
        fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
        fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
        fastaFileHandler.write(">DmelC:hr4_Blas=ter_Piler_1.0_Map_9\n")
        fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
        fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
        fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
        fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
        fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
        fastaFileHandler.close()

    def _writeChangeLogFile(self, changeLogFileName ):
        changeLogFileHandler = open(changeLogFileName, "w")
        changeLogFileHandler.write("ChangeLog of REPET\n")
        changeLogFileHandler.write("\n")
        changeLogFileHandler.write("\n")
        changeLogFileHandler.write("\n")
        changeLogFileHandler.write("REPET release 1.3.6\n")
        changeLogFileHandler.write("(release date XX/XX/2010)\n")
        changeLogFileHandler.write("\n")
        changeLogFileHandler.close()

    def _writeConfigFile(self, lineVersion):
        configFileHandler = open(self.configFileName, "w")
        configFileHandler.write("[repet_env]\n")
        configFileHandler.write(lineVersion)
        configFileHandler.write("repet_host: <your_MySQL_host>\n")
        configFileHandler.close()
        
        
test_suite = unittest.TestSuite()
test_suite.addTest( unittest.makeSuite( Test_CheckerUtils ) )
if __name__ == "__main__":
    unittest.TextTestRunner(verbosity=2).run( test_suite )