Mercurial > repos > yufei-luo > s_mart
view commons/core/coord/test/Test_AlignUtils.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# 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()