view commons/core/coord/test/Test_MatchUtils.py @ 31:0ab839023fe4

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# Copyright INRA (Institut National de la Recherche Agronomique)
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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 )