diff commons/core/checker/test/Test_CheckerUtils.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/checker/test/Test_CheckerUtils.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,535 @@
+# 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
+# abiding by the rules of distribution of free software.  You can  use, 
+# 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". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+
+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 )