Mercurial > repos > yufei-luo > s_mart
view commons/core/coord/test/Test_MatchUtils.py @ 17:b0e8584489e6
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author | m-zytnicki |
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date | Mon, 22 Apr 2013 11:11:10 -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 from commons.core.utils.FileUtils import FileUtils from commons.core.coord.MatchUtils import MatchUtils from commons.core.coord.Match import Match from commons.core.seq.BioseqDB import BioseqDB class Test_MatchUtils( unittest.TestCase ): def test_getMatchListFromFile( self ): inFile = "dummyInFile" inFileHandler = open( inFile, "w" ) inFileHandler.write( "query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n" ) m1 = Match() m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m1.write( inFileHandler ) m2 = Match() m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2.write( inFileHandler ) inFileHandler.close() lExp = [ m1, m2 ] lObs = MatchUtils.getMatchListFromFile( inFile ) self.assertEquals( lExp, lObs ) os.remove( inFile ) def test_getDictOfListsWithSubjectAsKey( self ): m1 = Match() m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2 = Match() m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) lMatch = [ m1, m2 ] dExp = { "SName1": [ m1 ], "SName2": [ m2 ] } dObs = MatchUtils.getDictOfListsWithSubjectAsKey( lMatch ) self.assertEquals( dExp, dObs ) def test_getDictOfListsWithQueryAsKey( self ): m1 = Match() m1.setFromTuple( ("QName1", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2 = Match() m2.setFromTuple( ("QName2", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m3 = Match() m3.setFromTuple( ("QName1", 1, 5, 5, 0.1, 0.2, "SName3", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) lMatch = [ m1, m2, m3 ] dExp = { "QName1": [ m1, m3 ], "QName2": [ m2 ] } dObs = MatchUtils.getDictOfListsWithQueryAsKey( lMatch ) self.assertEquals( dExp, dObs ) def test_getIdListFromMatchList( self ): m1 = Match() m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2 = Match() m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) ) lMatch = [ m1, m2 ] lExp = [1, 10] lObs = MatchUtils.getIdListFromMatchList( lMatch ) self.assertEquals(lExp, lObs) def test_getIdListFromMatchList_empty_list( self ): lMatch = [] lExp = [] lObs = MatchUtils.getIdListFromMatchList( lMatch ) self.assertEquals(lExp, lObs) def test_writeListInFile_without_header( self ): m1 = Match() m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2 = Match() m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) ) lMatch = [ m1, m2 ] line1 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName1\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t1\n" line2 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName2\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t10\n" expFileName = "expFileName.match" expFileHandle = open ( expFileName, 'w' ) expFileHandle.write(line1) expFileHandle.write(line2) expFileHandle.close() obsFileName = "obsFileName.match" MatchUtils.writeListInFile( lMatch, obsFileName ) self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) os.remove( obsFileName ) os.remove( expFileName ) def test_writeListInFile_with_header( self ): m1 = Match() m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2 = Match() m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) ) lMatch = [ m1, m2 ] headerLine = "query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n" line1 = headerLine line2 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName1\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t1\n" line3 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName2\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t10\n" expFileName = "expFileName.match" expFileHandle = open ( expFileName, 'w' ) expFileHandle.write(line1) expFileHandle.write(line2) expFileHandle.write(line3) expFileHandle.close() obsFileName = "obsFileName.match" MatchUtils.writeListInFile( lMatch, obsFileName, header=headerLine ) self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) os.remove( obsFileName ) os.remove( expFileName ) def test_writeListInFile_with_append_mode( self ): m1 = Match() m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2 = Match() m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 10) ) lMatch = [ m1, m2 ] line1 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName1\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t1\n" line2 = "QName\t1\t5\t5\t0.100000\t0.200000\tSName2\t5\t25\t20\t0.150000\t1e-20\t15\t87.200000\t10\n" expFileName = "expFileName.match" expFileHandle = open ( expFileName, 'w' ) expFileHandle.write(line1) expFileHandle.write(line1) expFileHandle.write(line2) expFileHandle.close() obsFileName = "obsFileName.match" obsFileHandle = open ( obsFileName, 'w' ) obsFileHandle.write(line1) obsFileHandle.close() MatchUtils.writeListInFile( lMatch, obsFileName, 'a' ) self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) os.remove( obsFileName ) os.remove( expFileName ) def test_rmvDuplicateMatches(self): m1 = Match() m1.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) m2 = Match() m2.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName2", 5, 25, 20, 0.15, 1e-20, 15, 86.2, 1) ) m3 = Match() m3.setFromTuple( ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1) ) lMatch = [ m1, m3, m2 ] lExp = [m1, m2] lObs = MatchUtils.rmvDuplicateMatches(lMatch) self.assertEquals(lExp, lObs) def test_filterDiffQrySbj_same_seq(self): fastaFileName = "file.fa" self._writeFastaFile(fastaFileName) qryDB = BioseqDB(fastaFileName) tabFileName = "file.tab" self._writeMatchFile(tabFileName) expListToKeep = ["HELITRON2"] obsListToKeep = MatchUtils.filterDiffQrySbj(qryDB,tabFileName, 0.95, 0.98, 2) self.assertEquals(expListToKeep, obsListToKeep) os.remove(fastaFileName) os.remove(tabFileName) def test_filterDiffQrySbj_TE_included_in_67percent_in_other_TE(self): fastaFileName = "file.fa" self._writeFastaFile2(fastaFileName) qryDB = BioseqDB(fastaFileName) tabFileName = "file.tab" self._writeMatchFile2(tabFileName) expListToKeep = [] obsListToKeep = MatchUtils.filterDiffQrySbj(qryDB, tabFileName, 0.95, 0.98, 2) self.assertEquals(expListToKeep, obsListToKeep) os.remove(fastaFileName) os.remove(tabFileName) def test_getNbDistinctSequencesInsideMatchesWithThresh_query(self): tabFileName = "file.tab" self._writeMatchFile3(tabFileName) lMatches = MatchUtils.getMatchListFromFile(tabFileName) expNbDistinctMatches = 1 obsNbDistinctMatches = MatchUtils.getNbDistinctSequencesInsideMatchesWithThresh(lMatches,0.95, 0.98,"query") self.assertEquals(expNbDistinctMatches, obsNbDistinctMatches) os.remove(tabFileName) def test_getNbDistinctSequencesInsideMatchesWithThresh_subject(self): tabFileName = "file.tab" self._writeMatchFile3(tabFileName) lMatches = MatchUtils.getMatchListFromFile(tabFileName) expNbDistinctMatches = 1 obsNbDistinctMatches = MatchUtils.getNbDistinctSequencesInsideMatchesWithThresh(lMatches,0.95, 0.98,"subject") self.assertEquals(expNbDistinctMatches, obsNbDistinctMatches) os.remove(tabFileName) def test_convertMatchFileToAlignFile(self): inputMatchFileName = "file.tab" expAlignFileName = "expected.align" obsAlignFileName = "file.align" self._writeExpAlignFile(expAlignFileName) self._writeMatchFile4(inputMatchFileName) MatchUtils.convertMatchFileToAlignFile(inputMatchFileName) self.assertTrue(FileUtils.are2FilesIdentical(expAlignFileName, obsAlignFileName)) os.remove(inputMatchFileName) os.remove(expAlignFileName) os.remove(obsAlignFileName) def test_convertMatchFileToAlignFile_empty_file(self): inputMatchFileName = "file.tab" expAlignFileName = "expected.align" obsAlignFileName = "file.align" f = open(expAlignFileName, "w") f.close() f = open(inputMatchFileName, "w") f.close() MatchUtils.convertMatchFileToAlignFile(inputMatchFileName) self.assertTrue(FileUtils.are2FilesIdentical(expAlignFileName, obsAlignFileName)) os.remove(inputMatchFileName) os.remove(expAlignFileName) os.remove(obsAlignFileName) def test_generateMatchFileWithNewPathId(self): inputMatchFileName = "file.tab" expMatchFileName = "expected.tab" obsMatchFileName = "obsFile.tab" self._writeMatchFile5(inputMatchFileName) self._writeExpMatchFile(expMatchFileName) MatchUtils.generateMatchFileWithNewPathId(inputMatchFileName, obsMatchFileName) self.assertTrue(FileUtils.are2FilesIdentical(expMatchFileName, obsMatchFileName)) os.remove(inputMatchFileName) os.remove(expMatchFileName) os.remove(obsMatchFileName) def test_generateMatchFileWithNewPathId_empty_file(self): inputMatchFileName = "file.tab" expMatchFileName = "expected.tab" obsMatchFileName = "obsFile.tab" f = open(expMatchFileName, "w") f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.close() f = open(inputMatchFileName, "w") f.close() MatchUtils.generateMatchFileWithNewPathId(inputMatchFileName, obsMatchFileName) self.assertTrue(FileUtils.are2FilesIdentical(expMatchFileName, obsMatchFileName)) os.remove(inputMatchFileName) os.remove(expMatchFileName) os.remove(obsMatchFileName) def test_convertMatchFileIntoABCFileOnQueryCoverage(self): matchFileName = "dummy.tab" with open(matchFileName, "w") as f: f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("chr3\t1\t100\t100\t0.98\t0.95\tchr5\t11\t110\t100\t0.95\t1e-52\t133\t87.200000\n") f.write("chr7\t1\t200\t200\t0.98\t0.95\tchr2\t11\t210\t200\t0.95\t1e-78\t235\t98.900000\n") f.write("chr5\t1\t100\t100\t0.95\t0.95\tchr3\t11\t110\t100\t0.98\t1e-52\t133\t87.200000\n") f.write("chr2\t1\t200\t200\t0.95\t0.95\tchr7\t11\t210\t200\t0.98\t1e-78\t235\t98.900000\n") expFileName = "exp.abc" with open(expFileName, "w") as f: f.write("chr3\tchr5\t0.98\n") f.write("chr7\tchr2\t0.98\n") f.write("chr5\tchr3\t0.95\n") f.write("chr2\tchr7\t0.95\n") obsFileName = "obs.abc" MatchUtils.convertMatchFileIntoABCFileOnQueryCoverage(matchFileName, obsFileName) self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) os.remove(matchFileName) os.remove(expFileName) os.remove(obsFileName) def test_convertMatchFileIntoABCFileOnQueryCoverage_coverage_threshold_85(self): matchFileName = "dummy.tab" with open(matchFileName, "w") as f: f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("chr3\t1\t100\t100\t0.98\t0.95\tchr5\t11\t110\t100\t0.95\t1e-52\t133\t87.200000\n") f.write("chr7\t1\t200\t200\t0.98\t0.95\tchr2\t11\t210\t200\t0.95\t1e-78\t235\t98.900000\n") f.write("chr5\t1\t100\t100\t0.85\t0.95\tchr3\t11\t110\t100\t0.98\t1e-52\t133\t87.200000\n") f.write("chr2\t1\t200\t200\t0.80\t0.95\tchr7\t11\t210\t200\t0.98\t1e-78\t235\t98.900000\n") expFileName = "exp.abc" with open(expFileName, "w") as f: f.write("chr3\tchr5\t0.98\n") f.write("chr7\tchr2\t0.98\n") f.write("chr5\tchr3\t0.85\n") obsFileName = "obs.abc" MatchUtils.convertMatchFileIntoABCFileOnQueryCoverage(matchFileName, obsFileName, coverage = 0.85) self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) os.remove(matchFileName) os.remove(expFileName) os.remove(obsFileName) def _writeFastaFile(self, fileName): f = open(fileName, "w") f.write(">HELITRON3\n") f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n") f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n") f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCTC\n") f.write(">HELITRON2\n") f.write("GGCCAGTCACAATGGGGGTTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGA\n") f.write("ATAAAAAATGATTATTTGCATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGG\n") f.write("GATTCGTTTCATTCACCGGATCTCTTGCGTCCGCCTCCGCCGTGCGACCTCCGCATTCTC\n") f.close() def _writeMatchFile(self, fileName): f = open(fileName, "w") f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("HELITRON3\t1\t180\t180\t1\t1\tHELITRON2\t1\t180\t180\t1\t2e-103\t357\t100\t1\n") f.close() def _writeFastaFile2(self, fileName): f = open(fileName, "w") f.write(">header2\n") f.write("TTTCACTGGTGTGTCATGCACATTTAATAGGGGTAAGACTGAATAAAAAATGATTATTTG\n") f.write("CATGAAATGGGGATGAGAGAGAAGGAAAGAGTTTCATCCTGGGATTCGTTTCATTCACCG\n") f.close() def _writeMatchFile2(self, fileName): f = open(fileName, "w") f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("header2\t1\t120\t120\t1\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n") f.close() def _writeMatchFile3(self, fileName): f = open(fileName, "w") f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n") f.write("header3\t1\t120\t120\t0.99\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-68\t238\t100\t1\n") f.write("header4\t1\t120\t120\t1\t0.94157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t67\t1\n") f.close() def _writeMatchFile4(self, fileName): f = open(fileName, "w") f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n") f.write("header3\t120\t220\t120\t0.99\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-65\t238\t100\t1\n") f.write("header4\t1\t120\t120\t1\t0.94157\tBS31790\t19\t138\t120\t0.674157\t3e-67\t244\t90\t1\n") f.close() def _writeExpAlignFile(self,fileName): f = open(fileName, "w") f.write("header2\t1\t120\tBS31790\t19\t138\t3e-68\t238.0\t100.0\n") f.write("header3\t120\t220\tBS31790\t19\t138\t3e-65\t238.0\t100.0\n") f.write("header4\t1\t120\tBS31790\t19\t138\t3e-67\t244.0\t90.0\n") f.close() def _writeMatchFile5(self,fileName): f = open(fileName, "w") f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n") f.write("header2\t124\t144\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100\t1\n") f.write("header3\t120\t220\t120\t0.99\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-65\t238\t100\t1\n") f.write("header4\t1\t120\t120\t1\t0.94157\tBS31790\t19\t138\t120\t0.674157\t3e-67\t244\t90\t1\n") f.close() def _writeExpMatchFile(self,fileName): f = open(fileName, "w") f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") f.write("header2\t1\t120\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100.000000\t1\n") f.write("header2\t124\t144\t120\t0.674157\t0.674157\tBS31790\t19\t138\t120\t0.674157\t3e-68\t238\t100.000000\t1\n") f.write("header3\t120\t220\t120\t0.990000\t0.994157\tBS31790\t19\t138\t120\t0.994157\t3e-65\t238\t100.000000\t2\n") f.write("header4\t1\t120\t120\t1.000000\t0.941570\tBS31790\t19\t138\t120\t0.674157\t3e-67\t244\t90.000000\t3\n") f.close() test_suite = unittest.TestSuite() test_suite.addTest( unittest.makeSuite( Test_MatchUtils ) ) if __name__ == "__main__": unittest.TextTestRunner(verbosity=2).run( test_suite )