view commons/pyRepetUnit/blastnForClassifierStep1/tests/Test_RepbaseBLRnForClassifierStep1.py @ 18:94ab73e8a190

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import unittest
import os
import shutil
import ConfigParser
import sys
from commons.pyRepetUnit.blastnForClassifierStep1.RepbaseBLRnForClassifierStep1 import RepbaseBLRnForClassifierStep1
from commons.core.utils.FileUtils import FileUtils
from commons.core.sql.DbFactory import DbFactory
from commons.core.sql.TablePathAdaptator import TablePathAdaptator
from commons.core.coord.Path import Path
import pyRepet.launcher.programLauncher

if not os.environ.has_key( "REPET_PATH" ):
    print "*** Error: no environment variable REPET_PATH"
    sys.exit(1)
sys.path.append( os.environ["REPET_PATH"] )

NB_EXPECTED_LINES_IN_PATH_FILE = 10
CURRENT_DIR = os.getcwd()


class Test_RepbaseBLRnForClassifierStep1( unittest.TestCase ):
    
    
    def setUp( self ):
        os.chdir(CURRENT_DIR)
        self._inFileName = "dummyFileName"
        self._launch_1 = "log = os.system( \""
        self._launch_2 = "\" )\n"
        self._launch_2 += "if log != 0:\n"
        self._launch_2 += "\tsys.exit(1)\n"
        self._cDir = "/home/user/dummy_cdir"
        self._tmpDir = "/home/user/dummy_tmpDir"
        self._configFileName = "configFile"
        self._repbaseName = "dummyRepbase_nt.fa"
        f = open(self._configFileName, "w")
        f.write("[repet_env]\n")
        f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
        f.write("repet_user: %s\n" % os.environ["REPET_USER"])
        f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
        f.write("repet_db: %s\n" % os.environ["REPET_DB"])
        f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
        f.write("[detect_features]\n")
        f.write("TE_BLRn: yes\n")
        f.write("TE_nucl_bank: %s\n" % self._repbaseName)
        f.write("wublast: yes\n")
        f.close()
        self._verbose = 0
        self._config = ConfigParser.ConfigParser()
        self._config.readfp( open(self._configFileName) )
        self._pL = pyRepet.launcher.programLauncher.programLauncher()
        self._project = "dummyProject"
        self._repbaseBLRn = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project)
        self._expFileName = "expFile"
        self._bank = self._config.get("detect_features","TE_nucl_bank")
        self._db = DbFactory.createInstance()
        
        
    def tearDown( self ):
        self._db.dropTable("%s_TE_BLRn_path" % (self._project))
        os.chdir(CURRENT_DIR)
        self._repbaseBLRn = None
        os.remove(self._configFileName)
        if os.path.isfile("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)):
            os.remove("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank))
        if os.path.isfile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)):
            os.remove("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank))
        if os.path.isfile("batch_1.fa_BLRn_%s.*" % (self._bank)):
            os.remove("batch_1.fa_BLRn_%s.*" % (self._bank))
        if os.path.isfile("batch_2.fa_BLRn_%s.*" % (self._bank)):
            os.remove("batch_2.fa_BLRn_%s.*" % (self._bank))
        if os.path.isfile("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank)):
            os.remove("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank))
        if os.path.isfile("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank)):
            os.remove("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank))
        if os.path.isfile(self._repbaseName):
            os.remove(self._repbaseName)
            os.remove(self._repbaseName + "_cut")
            os.remove(self._repbaseName + "_cut.xnd")
            os.remove(self._repbaseName + "_cut.xns")
            os.remove(self._repbaseName + "_cut.xnt")
            os.remove(self._repbaseName + ".Nstretch.map")
            os.remove("last_time_stamp.log")
        if os.path.isdir( "TE_BLRn" ):
            os.chdir( "TE_BLRn" )
            os.chdir(CURRENT_DIR)
            shutil.rmtree("TE_BLRn")
        if os.path.isfile(self._expFileName):
            os.remove(self._expFileName)
            
            
    def test_formatRepbase_ntIfNecessaryWithoutLog( self ):
        f = open(self._repbaseName, "w")
        f.write(">seq1\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.write(">seq2\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.close()
        f = open(self._expFileName, "w")
        f.write(">1  seq1 {Cut} 1..180\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.write(">2  seq2 {Cut} 1..180\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.close()
        self._repbaseBLRn.formatRepbase_ntIfNecessary()
        obsFileName = self._repbaseName + "_cut"
        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
        
        
    def test_formatRepbase_ntIfNecessary_withLogFile( self ):
        f = open(self._repbaseName, "w")
        f.write(">seq1\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.write(">seq2\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.close()
        f = open(self._expFileName, "w")
        f.write(">1  seq1 {Cut} 1..180\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.write(">2  seq2 {Cut} 1..180\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n")
        f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n")
        f.close()
        repbaseBLRnWithLog = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project)
        repbaseBLRnWithLog.formatRepbase_ntIfNecessary()
        obsFileName = self._repbaseName + "_cut"
        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
        
        
    def test_createCmdToLaunch( self ):
        bank = self._config.get("detect_features","TE_nucl_bank")
        obsCmd = self._repbaseBLRn.createCmdToLaunch()
        expCmd = self._launch_1 + os.environ["REPET_PATH"] + "/bin/blaster"
        expCmd += " -q %s" % ( self._inFileName )
        expCmd += " -s %s/%s" % ( self._cDir, bank )
        expCmd += " -B %s_BLRn_%s" % ( self._inFileName, bank )
        expCmd += " -n blastn"
        if self._config.get("detect_features","wublast") == "yes":
            expCmd += " -W"
        expCmd += " -r"
        expCmd += " -v 1"
        expCmd += self._launch_2
        expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.param\" ):\n" % ( self._cDir, self._inFileName, bank )
        expCmd += "\tos.system( \"mv %s_BLRn_%s.param %s\" )\n" % ( self._inFileName, bank, self._cDir )
        expCmd += "if os.path.exists( \"%s_cut\" ):\n" % ( self._inFileName )
        expCmd += "\tos.system( \"rm -f %s_cut*\" )\n" % ( self._inFileName )
        expCmd += "if os.path.exists( \"%s.Nstretch.map\" ):\n" % ( self._inFileName )
        expCmd += "\tos.remove( \"%s.Nstretch.map\" )\n" % ( self._inFileName )
        expCmd += "if os.path.exists( \"%s_BLRn_%s.raw\" ):\n" % ( self._inFileName, bank )
        expCmd += "\tos.remove( \"%s_BLRn_%s.raw\" )\n" % ( self._inFileName, bank )
        expCmd += "if os.path.exists( \"%s_BLRn_%s.seq_treated\" ):\n" % ( self._inFileName, bank )
        expCmd += "\tos.remove( \"%s_BLRn_%s.seq_treated\" )\n" % ( self._inFileName, bank )
        expCmd += self._launch_1
        expCmd += os.environ["REPET_PATH"] + "/bin/matcher"
        expCmd += " -m %s_BLRn_%s.align" % ( self._inFileName, bank )
        expCmd += " -q %s" % ( self._inFileName )
        expCmd += " -s %s/%s" % ( self._cDir, bank )
        expCmd += " -j"
        expCmd += " -v 1"
        expCmd += self._launch_2
        expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.path\" ):\n" % ( self._cDir, self._inFileName, bank )
        expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.path %s\" )\n" % ( self._inFileName, bank, self._cDir )
        expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.param\" ):\n" % ( self._cDir, self._inFileName, bank )
        expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.param %s\" )\n" % ( self._inFileName, bank, self._cDir )
        expCmd += "if os.path.exists( \"%s_BLRn_%s.align\" ):\n" % ( self._inFileName, bank )
        expCmd += "\tos.remove( \"%s_BLRn_%s.align\" )\n" % ( self._inFileName, bank )
        expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.fa\" ):\n" % ( self._inFileName, bank )
        expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.fa\" )\n" % ( self._inFileName, bank )
        expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.map\" ):\n" % ( self._inFileName, bank )
        expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.map\" )\n" % ( self._inFileName, bank )
        expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.tab\" ):\n" % ( self._inFileName, bank )
        expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.tab\" )\n" % ( self._inFileName, bank )
        if self._tmpDir != self._cDir:
            expCmd += "if os.path.exists( \"%s\" ):\n" % ( bank )
            expCmd += "\tos.remove( \"%s\" )\n" % ( bank )
        self.assertEquals( expCmd, obsCmd )
        
        
    def test_concatPathFile( self ):
        os.chdir(CURRENT_DIR)
        if not FileUtils.isRessourceExists("TE_BLRn"):
            os.mkdir( "TE_BLRn" )
        self._createPathFiles(self._bank)
        os.chdir( "TE_BLRn" )
        f = open(self._expFileName, "w")
        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.close()
        FileUtils.sortFileContent(self._expFileName)
        obsFileName = "%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)
        self._repbaseBLRn._concatPathFile(self._bank)
        FileUtils.sortFileContent(obsFileName)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
        
        
    def test_adaptIDInPathFile( self ):
        f = open("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank), "w")
        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.close()
        self._repbaseBLRn._adaptIDInPathFile(self._bank)
        f = open(self._expFileName, "w")
        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.close()
        obsFileName = "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName))
        
        
    def test_loadPathFileInTable( self ):
        os.chdir(CURRENT_DIR)
        if not FileUtils.isRessourceExists("TE_BLRn"):
            os.mkdir( "TE_BLRn" )
        self._createPathFiles(self._bank)
        os.chdir( "TE_BLRn" )
        f = open("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank), "w")
        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.close()
        self._repbaseBLRn._loadPathFileInTable(self._bank)
        resultFromFilePathList = self._readPathResultsFromFileAndFillList()
        resultFromTablePathList = self._readPathResultsFromTableAndFillList() 
        self.assertEquals(resultFromFilePathList, resultFromTablePathList)
        
        
    def test_findAndRemoveUselessFiles( self ):
        self._createFile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank))
        self._createFile("batch_1.fa_BLRn_%s.*" % (self._bank))
        self._createFile("batch_2.fa_BLRn_%s.*" % (self._bank))
        self._repbaseBLRn._findAndRemoveUselessFiles(self._bank)
        self.assertFalse(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)))
        self.assertFalse(FileUtils.isRessourceExists("batch_1.fa_BLRn_%s.*" % (self._bank)))
        self.assertFalse(FileUtils.isRessourceExists("batch_2.fa_BLRn_%s.*" % (self._bank)))
        
        
    def test_collectRepbaseBLRn( self ):
        os.chdir(CURRENT_DIR)
        if not FileUtils.isRessourceExists("TE_BLRn"):
            os.mkdir( "TE_BLRn" )
        self._createPathFiles(self._bank)
        os.chdir( "TE_BLRn" )
        self._repbaseBLRn.collectRepbaseBLRn()  
        self.assertTrue(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank )))
        self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, FileUtils.getNbLinesInSingleFile("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank )))
        self.assertTrue(self._db.doesTableExist("%s_TE_BLRn_path" % (self._project)))
        self._db.execute('select * from %s_TE_BLRn_path' % (self._project))
        self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, len(self._db.fetchall()))
        self._db.dropTable("%s_TE_BLRn_path" % (self._project))
        
        
    def _createPathFiles( self, bankFull ):
        bank = os.path.split(bankFull)[1]
        fileName = "batch_1.fa_BLRn_" + bank + ".align.clean_match.path"
        f = open(fileName, "w")
        f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.close()
        fileName = "batch_2.fa_BLRn_" + bank + ".align.clean_match.path"
        f = open(fileName, "w")
        f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n")
        f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n")
        f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n")
        f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n")
        f.close()
        
        
    def _readPathResultsFromTableAndFillList( self ):
        tablePathAdaptatorInstance = TablePathAdaptator (self._db, "%s_TE_BLRn_path" % (self._project))
        pathList = tablePathAdaptatorInstance.getListOfAllPaths()
        return pathList
    
    
    def _readPathResultsFromFileAndFillList( self ):
        pathInstance = Path()
        pathList = []
        f = open( "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank) , "r")
        while pathInstance.read( f ):
            pathList.append(pathInstance)
            pathInstance = Path()
        f.close()
        return pathList
   
   
    def _createFile( self, nameFile ):
        f = open(nameFile, "w")
        f.close()
        
        
test_suite = unittest.TestSuite()
test_suite.addTest( unittest.makeSuite( Test_RepbaseBLRnForClassifierStep1 ) )
if __name__ == "__main__":
    unittest.TextTestRunner(verbosity=2).run( test_suite )