diff smart_toolShed/commons/core/coord/test/Test_AlignUtils.py @ 0:e0f8dcca02ed

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/coord/test/Test_AlignUtils.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,777 @@
+# 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 time
+import shutil
+from commons.core.coord.AlignUtils import AlignUtils
+from commons.core.coord.Align import Align
+from commons.core.utils.FileUtils import FileUtils
+from commons.core.coord.Range import Range
+
+
+class Test_AlignUtils( unittest.TestCase ):
+    
+    def setUp( self ):
+        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
+        
+        
+    def tearDown( self ):
+        self._uniqId = ""
+        
+        
+    def test_getAlignListFromFile( self ):
+        a1 = Align()
+        a1.setFromTuple( ( "chr1", "1", "100", "seq3", "1", "100", "1e-23", "89", "97.26" ) )
+        a2 = Align()
+        a2.setFromTuple( ( "chr2", "121", "210", "seq5", "21", "110", "1e-32", "95", "98.13" ) )
+        
+        inFileName = "dummyFile_%s" % ( self._uniqId )
+        inFileHandler = open( inFileName, "w" )
+        a1.write( inFileHandler )
+        a2.write( inFileHandler )
+        inFileHandler.close()
+        
+        lExp = [ a1, a2 ]
+        lObs = AlignUtils.getAlignListFromFile( inFileName )
+        
+        self.assertEqual( lExp, lObs )
+        
+        if os.path.exists( inFileName ):
+            os.remove( inFileName )
+            
+            
+    def test_getListOfScores( self ):
+        a1 = Align()
+        a1.setFromTuple( ( "chr1", "1", "100", "seq3", "1", "100", "1e-23", "89", "97.26" ) )
+        a2 = Align()
+        a2.setFromTuple( ( "chr2", "121", "210", "seq5", "21", "110", "1e-32", "95", "98.13" ) )
+        lAligns = [ a1, a2 ]
+        
+        lExp = [ 89, 95 ]
+        lObs = AlignUtils.getListOfScores( lAligns )
+        
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_getScoreListFromFile( self ):
+        alignFile = "dummyAlignFile"
+        alignFileHandler = open( alignFile, "w" )
+        alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.2\n" )
+        alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.9\n" )
+        alignFileHandler.close()
+        
+        lExp = [ 133, 235 ]
+        lObs = AlignUtils.getScoreListFromFile( alignFile )
+        self.assertEqual( lExp, lObs )
+        
+        os.remove( alignFile )
+        
+        
+    def test_getScoreListFromFile_empty_file( self ):
+        alignFile = "dummyAlignFile"
+        alignFileHandler = open( alignFile, "w" )
+        alignFileHandler.close()
+        
+        lExp = []
+        lObs = AlignUtils.getScoreListFromFile( alignFile )
+        
+        self.assertEqual( lExp, lObs )
+        
+        os.remove( alignFile )
+        
+        
+    def test_getScoreListFromFile_with_endline_char( self ):
+        alignFile = "dummyAlignFile"
+        alignFileHandler = open( alignFile, "w" )
+        alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.2\n" )
+        alignFileHandler.write( "\n" )
+        alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.9\n" )
+        alignFileHandler.write( "\n" )
+        alignFileHandler.close()
+        
+        lExp = [133, 235]
+        lObs = AlignUtils.getScoreListFromFile( alignFile )
+        
+        self.assertEqual( lExp, lObs )
+        
+        os.remove( alignFile )
+        
+        
+    def test_convertAlignFileIntoMapFileWithQueriesAndSubjects( self ):
+        alignFile = "dummyAlignFile_%s" % ( self._uniqId )
+        alignFileHandler = open( alignFile, "w" )
+        alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.2\n" )
+        alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.9\n" )
+        alignFileHandler.close()
+        
+        expFile = "dummyExpFile_%s" % ( self._uniqId )
+        expFileHandler = open( expFile, "w" )
+        expFileHandler.write( "repet\tchr3\t1\t100\n" )
+        expFileHandler.write( "repet\tchr5\t11\t110\n" )
+        expFileHandler.write( "repet\tchr7\t1\t200\n" )
+        expFileHandler.write( "repet\tchr2\t11\t210\n" )
+        expFileHandler.close()
+        
+        obsFile = "dummyObsFile_%s" % ( self._uniqId )
+        
+        AlignUtils.convertAlignFileIntoMapFileWithQueriesAndSubjects( alignFile, obsFile )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        
+        for f in [ alignFile, expFile, obsFile ]:
+            if os.path.exists( f ):
+                os.remove( f )
+                
+                
+    def test_convertAlignFileIntoMapFileWithSubjectsOnQueries( self ):
+        alignFile = "dummyAlignFile_%s" % ( self._uniqId )
+        alignFileHandler = open( alignFile, "w" )
+        alignFileHandler.write( "chr3\t1\t100\tTE1\t11\t110\t1e-52\t133\t87.2\n" )
+        alignFileHandler.write( "chr7\t1\t200\tTE1\t11\t210\t1e-78\t235\t98.9\n" )
+        alignFileHandler.close()
+        
+        expFile = "dummyExpFile_%s" % ( self._uniqId )
+        expFileHandler = open( expFile, "w" )
+        expFileHandler.write( "TE1\tchr3\t1\t100\n" )
+        expFileHandler.write( "TE1\tchr7\t1\t200\n" )
+        expFileHandler.close()
+        
+        obsFile = "dummyObsFile_%s" % ( self._uniqId )
+        
+        AlignUtils.convertAlignFileIntoMapFileWithSubjectsOnQueries( alignFile, obsFile )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        
+        for f in [ alignFile, expFile, obsFile ]:
+            if os.path.exists( f ):
+                os.remove( f )
+                
+                
+    def test_getAlignListSortedByDecreasingScoreThenLength( self ):
+        a1 = Align()
+        a1.setFromTuple( ( "chr1", "1", "100", "seq3", "1", "100", "1e-23", "89", "97.26" ) )
+        a2 = Align()
+        a2.setFromTuple( ( "chr7", "121", "200", "seq9", "21", "110", "1e-32", "95", "98.13" ) )
+        a3 = Align()
+        a3.setFromTuple( ( "chr2", "121", "210", "seq5", "21", "110", "1e-32", "95", "98.13" ) )
+        lAligns = [ a1, a2, a3 ]
+        
+        lExp = [ a3, a2, a1 ]
+        
+        lObs = AlignUtils.getAlignListSortedByDecreasingScoreThenLength( lAligns )
+        
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_convertAlignFileIntoPathFile( self ):
+        alignFile = "dummyAlignFile_%s" % ( self._uniqId )
+        alignFileHandler = open( alignFile, "w" )
+        alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
+        alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
+        alignFileHandler.close()
+        
+        expFile = "dummyExpFile_%s" % ( self._uniqId )
+        expFileHandler = open( expFile, "w" )
+        expFileHandler.write( "1\tchr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
+        expFileHandler.write( "2\tchr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
+        expFileHandler.close()
+        
+        obsFile = "dummyObsFile_%s" % ( self._uniqId )
+        
+        AlignUtils.convertAlignFileIntoPathFile( alignFile, obsFile )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        
+        for f in [ alignFile, expFile, obsFile ]:
+            if os.path.exists( f ):
+                os.remove( f )
+                
+                
+    def test_sortAlignFile( self ):
+        alignFile = "dummyAlignFile_%s" % ( self._uniqId )
+        alignFileHandler = open( alignFile, "w" )
+        alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
+        alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
+        alignFileHandler.write( "chr8\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
+        alignFileHandler.write( "chr8\t1\t100\tchr5\t15\t90\t1e-52\t133\t87.200000\n" )
+        alignFileHandler.write( "chr8\t1\t100\tchr5\t11\t100\t1e-52\t133\t87.200000\n" )
+        alignFileHandler.close()
+        
+        expFile = "dummyExpFile_%s" % ( self._uniqId )
+        expFileHandler = open( expFile, "w" )
+        expFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
+        expFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
+        expFileHandler.write( "chr8\t1\t100\tchr5\t11\t100\t1e-52\t133\t87.200000\n" )
+        expFileHandler.write( "chr8\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
+        expFileHandler.write( "chr8\t1\t100\tchr5\t15\t90\t1e-52\t133\t87.200000\n" )
+        expFileHandler.close()
+        
+        obsFile = "dummyObsFile_%s" % ( self._uniqId )
+        
+        AlignUtils.sortAlignFile( alignFile, obsFile )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        
+        for f in [ alignFile, expFile, obsFile ]:
+            if os.path.exists( f ):
+                os.remove( f )
+    
+    def test_writeListInFile( self ):
+        line1 = ("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
+        line2 = ("chr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
+        line3 = ("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
+        
+        expFileName = "expFileName.align"
+        expFileHandle = open ( expFileName, 'w' )
+        expFileHandle.write(line1)
+        expFileHandle.write(line2)
+        expFileHandle.write(line3)
+        expFileHandle.close()
+        
+        iAlign1 = Align()
+        iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign2 = Align()
+        iAlign2.setFromString("chr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign3 = Align()
+        iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        
+        obsFileName = "obsFileName.align"
+        obsPathList =[iAlign1, iAlign2, iAlign3] 
+        
+        AlignUtils.writeListInFile( obsPathList, obsFileName )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
+        
+        os.remove( obsFileName )
+        os.remove( expFileName )
+        
+        
+    def test_splitAlignListByQueryName_empty_list( self ):
+        lAlign = []
+        
+        obsLAlign = AlignUtils.splitAlignListByQueryName( lAlign )
+        
+        expLAlign = []
+        
+        self.assertEquals( expLAlign, obsLAlign )
+        
+        
+    def test_splitAlignListByQueryName( self ):
+        iAlign1 = Align()
+        iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign2 = Align()
+        iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign3 = Align()
+        iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        lAlign = [ iAlign1, iAlign2, iAlign3 ]
+        
+        obsLAlign = AlignUtils.splitAlignListByQueryName( lAlign )
+        
+        expLAlign = [ [ iAlign1, iAlign3 ],
+                     [ iAlign2 ] ]
+        
+        self.assertEquals( expLAlign, obsLAlign )
+        
+        
+    def test_splitAlignListByQueryName_last_align_alone( self ):
+        iAlign1 = Align()
+        iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign2 = Align()
+        iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign3 = Align()
+        iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign4 = Align()
+        iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign5 = Align()
+        iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign6 = Align()
+        iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign7 = Align()
+        iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign8 = Align()
+        iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign9 = Align()
+        iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        lAlign = [ iAlign1, iAlign2, iAlign3, iAlign4, iAlign5, iAlign6, iAlign7, iAlign8, iAlign9 ]
+
+        obsLAlign = AlignUtils.splitAlignListByQueryName( lAlign )
+        
+        expLAlign = [ [ iAlign1, iAlign3, iAlign6, iAlign7 ],
+                     [ iAlign2, iAlign5, iAlign8 ],
+                     [ iAlign4 ],
+                     [ iAlign9 ] ]
+        
+        self.assertEquals( expLAlign, obsLAlign )
+        
+        
+    def test_createAlignFiles( self ):
+        expFile1 = "dummyExpAlignFile.align_1"
+        expFile2 = "dummyExpAlignFile.align_2"
+        expFile3 = "dummyExpAlignFile.align_3"
+        expFile4 = "dummyExpAlignFile.align_4"
+        
+        f1 = open(expFile1, "w")
+        iAlign1 = Align()
+        iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign1.write(f1)
+        iAlign3 = Align()
+        iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign3.write(f1)
+        iAlign6 = Align()
+        iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign6.write(f1)
+        iAlign7 = Align()
+        iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign7.write(f1)
+        f1.close()
+        
+        f2 = open(expFile2, "w")
+        iAlign2 = Align()
+        iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign2.write(f2)
+        iAlign5 = Align()
+        iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign5.write(f2)
+        iAlign8 = Align()
+        iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign8.write(f2)
+        f2.close()
+        
+        f3 = open(expFile3, "w")
+        iAlign4 = Align()
+        iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign4.write(f3)
+        f3.close()
+        
+        f4 = open(expFile4, "w")
+        iAlign9 = Align()
+        iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign9.write(f4)
+        f4.close()
+        
+        lAlignList = [ [ iAlign1, iAlign3, iAlign6, iAlign7 ],
+                      [ iAlign2, iAlign5, iAlign8 ],
+                      [ iAlign4 ],
+                      [ iAlign9 ] ]
+        
+        AlignUtils.createAlignFiles( lAlignList, "dummyAlignFile" )
+        
+        obsFile1 = "dummyAlignFile_1.align"
+        obsFile2 = "dummyAlignFile_2.align"
+        obsFile3 = "dummyAlignFile_3.align"
+        obsFile4 = "dummyAlignFile_4.align"
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
+        
+        os.remove(expFile1)
+        os.remove(expFile2)
+        os.remove(expFile3)
+        os.remove(expFile4)
+        os.remove(obsFile1)
+        os.remove(obsFile2)
+        os.remove(obsFile3)
+        os.remove(obsFile4)
+        
+
+    def test_createAlignFiles_eleven_output_files( self ):
+        expFile1 = "dummyExpAlignFile.align_01"
+        expFile2 = "dummyExpAlignFile.align_02"
+        expFile3 = "dummyExpAlignFile.align_03"
+        expFile4 = "dummyExpAlignFile.align_04"
+        expFile5 = "dummyExpAlignFile.align_05"
+        expFile6 = "dummyExpAlignFile.align_06"
+        expFile7 = "dummyExpAlignFile.align_07"
+        expFile8 = "dummyExpAlignFile.align_08"
+        expFile9 = "dummyExpAlignFile.align_09"
+        expFile10 = "dummyExpAlignFile.align_10"
+        expFile11 = "dummyExpAlignFile.align_11"
+        lExpFiles = [expFile1, expFile2, expFile3, expFile4, expFile5, expFile6, expFile7, expFile8, expFile9, expFile10, expFile11]
+        
+        f1 = open(expFile1, "w")
+        iAlign1 = Align()
+        iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign1.write(f1)
+        f1.close()
+        
+        f2 = open(expFile2, "w")
+        iAlign2 = Align()
+        iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign2.write(f2)
+        f2.close()
+        
+        f3 = open(expFile3, "w")
+        iAlign3 = Align()
+        iAlign3.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign3.write(f3)
+        f3.close()
+        
+        f4 = open(expFile4, "w")
+        iAlign4 = Align()
+        iAlign4.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign4.write(f4)
+        f4.close()
+        
+        f = open(expFile5, "w")
+        iAlign5 = Align()
+        iAlign5.setFromString("chr5\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign5.write(f)
+        f.close()
+        
+        f = open(expFile6, "w")
+        iAlign6 = Align()
+        iAlign6.setFromString("chr6\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign6.write(f)
+        f.close()
+        
+        f = open(expFile7, "w")
+        iAlign7 = Align()
+        iAlign7.setFromString("chr7\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign7.write(f)
+        f.close()
+        
+        f = open(expFile8, "w")
+        iAlign8 = Align()
+        iAlign8.setFromString("chr8\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign8.write(f)
+        f.close()
+        
+        f = open(expFile9, "w")
+        iAlign9 = Align()
+        iAlign9.setFromString("chr9\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign9.write(f)
+        f.close()
+        
+        f = open(expFile10, "w")
+        iAlign10 = Align()
+        iAlign10.setFromString("chr10\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign10.write(f)
+        f.close()
+        
+        f = open(expFile11, "w")
+        iAlign11 = Align()
+        iAlign11.setFromString("chr11\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign11.write(f)
+        f.close()
+        
+        lAlignList = [[iAlign1], [iAlign2], [iAlign3], [iAlign4], [iAlign5], [iAlign6], [iAlign7], [iAlign8], [iAlign9], [iAlign10], [iAlign11]]
+        
+        AlignUtils.createAlignFiles(lAlignList, "dummyAlignFile")
+
+        obsFile1 = "dummyAlignFile_01.align"
+        obsFile2 = "dummyAlignFile_02.align"
+        obsFile3 = "dummyAlignFile_03.align"
+        obsFile4 = "dummyAlignFile_04.align"
+        obsFile5 = "dummyAlignFile_05.align"
+        obsFile6 = "dummyAlignFile_06.align"
+        obsFile7 = "dummyAlignFile_07.align"
+        obsFile8 = "dummyAlignFile_08.align"
+        obsFile9 = "dummyAlignFile_09.align"
+        obsFile10 = "dummyAlignFile_10.align"
+        obsFile11 = "dummyAlignFile_11.align"
+        lObsFiles = [obsFile1, obsFile2, obsFile3, obsFile4, obsFile5, obsFile6, obsFile7, obsFile8, obsFile9, obsFile10, obsFile11]
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile5, obsFile5 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile6, obsFile6 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile7, obsFile7 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile8, obsFile8 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile9, obsFile9 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile10, obsFile10 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile11, obsFile11 ) )
+        
+        for file in lExpFiles:
+            os.remove(file)
+        for file in lObsFiles:
+            os.remove(file)
+            
+            
+    def test_createAlignFiles_dirName_specified( self ):
+        expFile1 = "dummyExpAlignFile.align_1"
+        expFile2 = "dummyExpAlignFile.align_2"
+        expFile3 = "dummyExpAlignFile.align_3"
+        expFile4 = "dummyExpAlignFile.align_4"
+        
+        f1 = open(expFile1, "w")
+        iAlign1 = Align()
+        iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign1.write(f1)
+        iAlign3 = Align()
+        iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign3.write(f1)
+        iAlign6 = Align()
+        iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign6.write(f1)
+        iAlign7 = Align()
+        iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign7.write(f1)
+        f1.close()
+        
+        f2 = open(expFile2, "w")
+        iAlign2 = Align()
+        iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign2.write(f2)
+        iAlign5 = Align()
+        iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign5.write(f2)
+        iAlign8 = Align()
+        iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign8.write(f2)
+        f2.close()
+        
+        f3 = open(expFile3, "w")
+        iAlign4 = Align()
+        iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign4.write(f3)
+        f3.close()
+        
+        f4 = open(expFile4, "w")
+        iAlign9 = Align()
+        iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign9.write(f4)
+        f4.close()
+        
+        lAlignList = [[iAlign1, iAlign3, iAlign6, iAlign7], [iAlign2, iAlign5, iAlign8], [iAlign4], [iAlign9]]
+ 
+        dirName = "dummyAlignDir"    
+            
+        AlignUtils.createAlignFiles(lAlignList, "dummyAlignFile", dirName)
+
+        obsFile1 = dirName + "/dummyAlignFile_1.align"
+        obsFile2 = dirName + "/dummyAlignFile_2.align"
+        obsFile3 = dirName + "/dummyAlignFile_3.align"
+        obsFile4 = dirName + "/dummyAlignFile_4.align"
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
+        
+        os.remove(expFile1)
+        os.remove(expFile2)
+        os.remove(expFile3)
+        os.remove(expFile4)
+        shutil.rmtree (dirName)
+        
+        
+    def test_createAlignFiles_dirName_specified_with_ended_slash( self ):
+        expFile1 = "dummyExpAlignFile.align_1"
+        expFile2 = "dummyExpAlignFile.align_2"
+        expFile3 = "dummyExpAlignFile.align_3"
+        expFile4 = "dummyExpAlignFile.align_4"
+        
+        f1 = open(expFile1, "w")
+        iAlign1 = Align()
+        iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign1.write(f1)
+        iAlign3 = Align()
+        iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign3.write(f1)
+        iAlign6 = Align()
+        iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign6.write(f1)
+        iAlign7 = Align()
+        iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign7.write(f1)
+        f1.close()
+        
+        f2 = open(expFile2, "w")
+        iAlign2 = Align()
+        iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign2.write(f2)
+        iAlign5 = Align()
+        iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign5.write(f2)
+        iAlign8 = Align()
+        iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign8.write(f2)
+        f2.close()
+        
+        f3 = open(expFile3, "w")
+        iAlign4 = Align()
+        iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign4.write(f3)
+        f3.close()
+        
+        f4 = open(expFile4, "w")
+        iAlign9 = Align()
+        iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
+        iAlign9.write(f4)
+        f4.close()
+        
+        lAlignList = [[iAlign1, iAlign3, iAlign6, iAlign7], [iAlign2, iAlign5, iAlign8], [iAlign4], [iAlign9]]
+ 
+        dirName = "dummyAlignDir/"    
+            
+        AlignUtils.createAlignFiles(lAlignList, "dummyAlignFile", dirName)
+
+        obsFile1 = dirName + "dummyAlignFile_1.align"
+        obsFile2 = dirName + "dummyAlignFile_2.align"
+        obsFile3 = dirName + "dummyAlignFile_3.align"
+        obsFile4 = dirName + "dummyAlignFile_4.align"
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
+        
+        os.remove(expFile1)
+        os.remove(expFile2)
+        os.remove(expFile3)
+        os.remove(expFile4)
+        shutil.rmtree (dirName)
+        
+        
+    def test_sortList( self ):
+        iAlign1 = Align( Range("qry1",3,80), Range("sbj1",3,80), 1e-20, 103, 97.3 )  # higher query start
+        iAlign2 = Align( Range("qry1",1,100), Range("sbj1",1,100), 1e-20, 113, 97.3 )  # higher score
+        iAlign3 = Align( Range("qry2",1,100), Range("sbj1",1,100), 1e-20, 103, 97.3 )  # different query
+        iAlign4 = Align( Range("qry1",1,100), Range("sbj1",1,100), 1e-20, 103, 97.3 )  # canonical
+        iAlign5 = Align( Range("qry1",1,100), Range("sbj2",1,100), 1e-20, 103, 97.3 )  # different subject
+        iAlign6 = Align( Range("qry1",201,300), Range("sbj1",100,1), 1e-20, 103, 97.3 )  # subject on reverse strand
+        iAlign7 = Align( Range("qry1",401,500), Range("sbj1",1,100), 1e-20, 103, 97.3 )  # higher query start
+        lAligns = [ iAlign1, iAlign2, iAlign3, iAlign4, iAlign5, iAlign6, iAlign7 ]
+        lExp = [iAlign4, iAlign2, iAlign1, iAlign6, iAlign7, iAlign5, iAlign3]
+        lObs = AlignUtils.sortList( lAligns )
+        self.assertEquals( lExp, lObs )
+        
+        
+    def test_isOverlapping( self ):
+        iAlign1 = Align( Range("chr1",1,100), Range("TE1",11,110), 1e-20, 90.2, 30 )
+        iAlign2 = Align( Range("chr1",51,80), Range("TE1",61,90), 1e-20, 90.2, 30 )
+        self.assertTrue( iAlign1.isOverlapping( iAlign2 ) )
+        
+        iAlign1 = Align( Range("chr1",1,100), Range("TE1",11,110), 1e-20, 90.2, 30 )
+        iAlign2 = Align( Range("chr1",51,80), Range("TE1",161,190), 1e-20, 90.2, 30 )
+        self.assertFalse( iAlign1.isOverlapping( iAlign2 ) )
+        
+        
+    def test_mergeList( self ):
+        iAlign1 = Align( Range("chr1",81,120), Range("TE1",91,130), 1e-20, 90.2, 30 )
+        iAlign2 = Align( Range("chr2",51,80), Range("TE1",61,90), 1e-20, 90.2, 30 )  # different query
+        iAlign3 = Align( Range("chr1",1,100), Range("TE1",11,110), 1e-20, 90.2, 30 )  # to be merged with 1st line
+        iAlign4 = Align( Range("chr1",1,200), Range("TE2",11,210), 1e-20, 90.2, 30 )  # different subject
+        iAlign5 = Align( Range("chr1",1,100), Range("TE1",501,600), 1e-20, 90.2, 30 )  # non-overlapping subject
+        lAligns = [ iAlign1, iAlign2, iAlign3, iAlign4, iAlign5 ]
+        
+        iAlign6 = Align( Range("chr1",1,120), Range("TE1",11,130), 1e-20, 90.2, 30 )
+        lExp = [ iAlign6, iAlign5, iAlign4, iAlign2 ]
+        
+        lObs = AlignUtils.mergeList( lAligns )
+        
+        self.assertEquals( lExp, lObs )
+        
+        
+    def test_mergeFile_empty( self ):
+        inFile = "dummyInFile.align"
+        inF = open( inFile, "w" )
+        inF.close()
+        
+        expFile = "dummyExpFile.align"
+        expF = open( expFile, "w" )
+        expF.close()
+        
+        obsFile = "dummyObsFile.align"
+        AlignUtils.mergeFile( inFile, obsFile )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        
+        for f in [ inFile, expFile, obsFile ]:
+            os.remove( f )
+            
+            
+    def test_mergeFile( self ):
+        iAlign = Align()
+        
+        inFile = "dummyInFile.align"
+        inF = open( inFile, "w" )
+        iAlign.setFromString( "chr1\t81\t120\tTE1\t91\t130\t1e-20\t30\t90.2\n" )
+        iAlign.write( inF )
+        iAlign.setFromString( "chr2\t51\t80\tTE1\t61\t90\t1e-20\t30\t90.2\n" )  # different query
+        iAlign.write( inF )
+        iAlign.setFromString( "chr1\t1\t100\tTE1\t11\t110\t1e-20\t30\t90.2\n" )  # to be merged with 1st line
+        iAlign.write( inF )
+        iAlign.setFromString( "chr1\t1\t200\tTE2\t11\t210\t1e-20\t30\t90.2\n" )  # different subject
+        iAlign.write( inF )
+        inF.close()
+        
+        expFile = "dummyExpFile.align"
+        expF = open( expFile, "w" )
+        iAlign.setFromString( "chr1\t1\t120\tTE1\t11\t130\t1e-20\t30\t90.2\n" )
+        iAlign.write( expF )
+        iAlign.setFromString( "chr1\t1\t200\tTE2\t11\t210\t1e-20\t30\t90.2\n" )
+        iAlign.write( expF )
+        iAlign.setFromString( "chr2\t51\t80\tTE1\t61\t90\t1e-20\t30\t90.2\n" )
+        iAlign.write( expF )
+        expF.close()
+        
+        obsFile = "dummyObsFile.align"
+        AlignUtils.mergeFile( inFile, obsFile )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        
+        for f in [ inFile, expFile, obsFile ]:
+            os.remove( f )
+            
+            
+    def test_updateScoresInFile( self ):
+        iAlign = Align()
+        
+        inFile = "dummyInFile.align"
+        inHandler = open( inFile, "w" )
+        iAlign.setFromString( "query1\t1\t100\tsubject1\t1\t95\t1e-180\t230\t90.2\n" )
+        iAlign.write( inHandler )
+        inHandler.close()
+        
+        expFile = "dummyExpFile.align"
+        expHandler = open( expFile, "w" )
+        iAlign.setFromString( "query1\t1\t100\tsubject1\t1\t95\t1e-180\t%i\t90.2\n" % ( ( 100 - 1 + 1 ) * 90.2 / 100.0 ) )
+        iAlign.write( expHandler )
+        expHandler.close()
+        
+        obsFile = "dummyObsFile.align"
+        AlignUtils.updateScoresInFile( inFile, obsFile )
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        
+        for f in [ inFile, expFile, obsFile ]:
+            os.remove( f )
+            
+            
+if __name__ == "__main__":
+    unittest.main()
\ No newline at end of file