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view commons/core/seq/test/Test_AlignedBioseqDB.py @ 6:769e306b7933
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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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 sys import os import time from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB from commons.core.seq.Bioseq import Bioseq from commons.core.utils.FileUtils import FileUtils from commons.core.coord.Align import Align from commons.core.coord.Range import Range from commons.core.stat.Stat import Stat class Test_AlignedBioseqDB( unittest.TestCase ): def setUp( self ): self._i = AlignedBioseqDB() self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) def tearDown( self ): self._i = None self._uniqId = "" def test_getLength(self): iAlignedBioseqDB = AlignedBioseqDB() iBioseq1 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) iAlignedBioseqDB.setData([iBioseq1]) expLenght = 29 obsLength = iAlignedBioseqDB.getLength() self.assertEquals(expLenght, obsLength) def test_getSeqLengthWithoutGaps( self ): iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.add( Bioseq( "seq3", "AGCG-GACGATGCAGCAT--GCGAATGA--CGAT" ) ) expLenght = 29 obsLength = iAlignedBioseqDB.getSeqLengthWithoutGaps( "seq3" ) self.assertEquals(expLenght, obsLength) def test_getListOccPerSite(self): iBioseq1 = Bioseq( "seq1", "AGAAA") iBioseq2 = Bioseq( "seq2", "TCAAG") iBioseq3 = Bioseq( "seq3", "GGTAC") iBioseq4 = Bioseq( "seq4", "CCTTA") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expList = [ {"A":1, "T":1, "G":1, "C":1}, {"G":2, "C":2}, {"A":2, "T":2 }, {"A":3, "T":1 }, {"A":2, "G":1, "C":1} ] obsList = iAlignedBioseqDB.getListOccPerSite() self.assertEquals(expList, obsList) def test_getListOccPerSite_with_none_sequence(self): iBioseq1 = Bioseq( "seq1", "AGAAA") iBioseq2 = Bioseq( "seq2", "TCAAG") iBioseq3 = Bioseq( "seq3", "GGTAC") iBioseq4 = Bioseq( "seq4", None) iBioseq5 = Bioseq( "seq5", "CCTTA") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4, iBioseq5]) expList = [ {"A":1, "T":1, "G":1}, {"G":2, "C":1}, {"A":2, "T":1 }, {"A":3}, {"A":1, "G":1, "C":1}, ] obsList = iAlignedBioseqDB.getListOccPerSite() self.assertEquals(expList, obsList) def test_getListOccPerSite_on_three_sequence(self): iBioseq1 = Bioseq( "seq1", "AGAAA") iBioseq2 = Bioseq( "seq2", "TCAAG") iBioseq3 = Bioseq( "seq3", "GGTAC") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) expList = [ {"A":1, "T":1, "G":1}, {"G":2, "C":1}, {"A":2, "T":1 }, {"A":3}, {"A":1, "G":1, "C":1}, ] obsList = iAlignedBioseqDB.getListOccPerSite() self.assertEquals(expList, obsList) def test_getConsensus_with_minNbNt_greater_than_nbInSeq(self): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "TGCA") iBioseq3 = Bioseq("seq3", "TACT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) expConsensus = Bioseq("consensus= length=4 nbAlign=3","TGCT") obsConsensus = iAlignedBioseqDB.getConsensus(5) self.assertEquals(expConsensus, obsConsensus) def test_getConsensus_with_minPropNt_greater_than_1(self): isSysExitRaised = False iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "TGCA") iBioseq3 = Bioseq("seq3", "TACT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) expFileName = "expFileName" expFileHandler = open(expFileName,"w") expMessage = "ERROR: minPropNt=2.00 should be a proportion (below 1.0)\n" expFileHandler.write(expMessage) expFileHandler.close() obsFileName = "obsFileName" obsFileHandler = open(obsFileName,"w") stdoutRef = sys.stdout sys.stdout = obsFileHandler try: iAlignedBioseqDB.getConsensus(2,2) except SystemExit: isSysExitRaised = True obsFileHandler.close() expFileHandler.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) self.assertTrue( isSysExitRaised ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) stdoutRef = sys.stdout def test_getConsensus_with_AlignBioseqInstance_size_1(self): isSysExitRaised = False iBioseq1 = Bioseq("seq1", "AGAT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1]) expFileName = "expFileName" expFileHandler = open(expFileName,"w") expMessage = "ERROR: can't make a consensus with less than 2 sequences\n" expFileHandler.write(expMessage) expFileHandler.close() obsFileName = "obsFileName" obsFileHandler = open(obsFileName,"w") stdoutRef = sys.stdout sys.stdout = obsFileHandler try: iAlignedBioseqDB.getConsensus(4) except SystemExit: isSysExitRaised = True obsFileHandler.close() expFileHandler.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) self.assertTrue( isSysExitRaised ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) stdoutRef = sys.stdout def test_getConsensus_with_gap_assertion_on_warning_msg(self): iBioseq1 = Bioseq("seq1", "A-GA-T") iBioseq2 = Bioseq("seq2", "T-GC-A") iBioseq3 = Bioseq("seq3", "T-AC-T") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) expFileName = "expFileName" expFileHandler = open(expFileName,"w") expMessage = "WARNING: 2 sites were removed (33.33%)\n" expFileHandler.write(expMessage) expFileHandler.close() obsFileName = "obsFileName" obsFileHandler = open(obsFileName,"w") stdoutRef = sys.stdout sys.stdout = obsFileHandler iAlignedBioseqDB.getConsensus(2) obsFileHandler.close() expFileHandler.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) stdoutRef = sys.stdout def test_getConsensus_with_gap_assertion_on_result(self): iBioseq1 = Bioseq("seq1", "A-GA-T") iBioseq2 = Bioseq("seq2", "T-GC-A") iBioseq3 = Bioseq("seq3", "T-AC-T") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) expConsensus = Bioseq("consensus= length=4 nbAlign=3","TGCT") obsConsensus = iAlignedBioseqDB.getConsensus(2) self.assertEquals(expConsensus, obsConsensus) def test_getConsensus_with_gaps_and_no_consensus_built_assertion_on_result(self): iBioseq1 = Bioseq("seq1", "A--A-T") iBioseq2 = Bioseq("seq2", "----A-") iBioseq3 = Bioseq("seq3", "--A---") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) expConsensus = None obsConsensus = iAlignedBioseqDB.getConsensus(2) self.assertEquals(expConsensus, obsConsensus) def test_getConsensus_with_gaps_and_no_consensus_built_assertion_on_warning_messages(self): iBioseq1 = Bioseq("seq1", "A--A-T") iBioseq2 = Bioseq("seq2", "----A-") iBioseq3 = Bioseq("seq3", "--A---") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) expFileName = "expFileName" expFileHandler = open(expFileName,"w") expMessage1 = "WARNING: 1 site was removed (16.67%)\n" expMessage2 = "WARNING: no consensus can be built (no sequence left)\n" expFileHandler.write(expMessage1) expFileHandler.write(expMessage2) expFileHandler.close() obsFileName = "obsFileName" obsFileHandler = open(obsFileName,"w") stdoutRef = sys.stdout sys.stdout = obsFileHandler iAlignedBioseqDB.getConsensus(2) obsFileHandler.close() expFileHandler.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) stdoutRef = sys.stdout def test_getConsensus_with_unacceptable_N_proportion_assertion_on_result(self): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "CCCA") iBioseq3 = Bioseq("seq3", "TTCT") iBioseq4 = Bioseq("seq4", "TTAT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expConsensus = None obsConsensus = iAlignedBioseqDB.getConsensus(2,0.75) self.assertEquals(expConsensus, obsConsensus) def test_getConsensus_with_unacceptable_N_proportion_assertion_on_warning_msg(self): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "CCCA") iBioseq3 = Bioseq("seq3", "TTCT") iBioseq4 = Bioseq("seq4", "TTAT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expFileName = "expFileName" expFileHandler = open(expFileName,"w") expMessage = "WARNING: no consensus can be built (75% of N's >= 40%)\n" expFileHandler.write(expMessage) expFileHandler.close() obsFileName = "obsFileName" obsFileHandler = open(obsFileName,"w") stdoutRef = sys.stdout sys.stdout = obsFileHandler iAlignedBioseqDB.getConsensus(2,0.75) obsFileHandler.close() expFileHandler.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) stdoutRef = sys.stdout def test_getConsensus_with_acceptable_N_proportion_assertion_on_warning_msg(self): iBioseq1 = Bioseq("seq1", "AGATAA") iBioseq2 = Bioseq("seq2", "CTCAAA") iBioseq3 = Bioseq("seq3", "TTCTAA") iBioseq4 = Bioseq("seq4", "GTATCC") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expFileName = "expFileName" expFileHandler = open(expFileName,"w") expMessage = "WARNING: 33% of N's\n" expFileHandler.write(expMessage) expFileHandler.close() obsFileName = "obsFileName" obsFileHandler = open(obsFileName,"w") stdoutRef = sys.stdout sys.stdout = obsFileHandler iAlignedBioseqDB.getConsensus(2,0.6) obsFileHandler.close() expFileHandler.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) sys.stdout = stdoutRef os.remove ( obsFileName ) os.remove ( expFileName ) stdoutRef = sys.stdout def test_getConsensus_with_acceptable_N_proportion_assertion_on_result(self): iBioseq1 = Bioseq("seq1", "AGATAA") iBioseq2 = Bioseq("seq2", "CTCAAA") iBioseq3 = Bioseq("seq3", "TTCTAA") iBioseq4 = Bioseq("seq4", "GTATCC") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expConsensus = Bioseq("consensus= length=6 nbAlign=4","NTNTAA") obsConsensus = iAlignedBioseqDB.getConsensus(2,0.6) self.assertEquals(expConsensus, obsConsensus) def test_getConsensus_with_chimeric_seq_in_alignment(self): iBioseq1 = Bioseq("seq1", "AGAGTTGTAA") iBioseq2 = Bioseq("seq2", "ATC----AAA") iBioseq3 = Bioseq("seq3", "ATC----TAA") iBioseq4 = Bioseq("seq4", "GTC----TAA") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expConsensus = Bioseq("consensus= length=6 nbAlign=4","ATCTAA") obsConsensus = iAlignedBioseqDB.getConsensus(2) self.assertEquals(expConsensus, obsConsensus) def test_getConsensus_with_SATannot_data(self): iBioseq1 = Bioseq("MbS69Gr8Cl511 chunk21 {Fragment} 165740..165916", "--TTTAGCCGAAGTCCATATGAGTCTTTGTGTTTGTATCTTCTAACAAGGAAACACTACTTAGGCTTTTAGGATAAGATTGCGGTTTAAGTTCTTATACTCAATCATACACATGACATCAAGTCATATTCGAATCCAAAACTCTAAGCAAGCTTCTTCTTGCTTCTCAAA-GCTTTGATG") iBioseq2 = Bioseq("MbS68Gr8Cl511 chunk21 {Fragment} 165916..166092", "GGTCTAGCCGAAGTCCATATGAGTCTTTGTCTTTGTATCTTCTAACAAGAAAACACTACTTAGGCTTTTAGGATAAGGTTGCAGTTTAAGTTTTTATACTAAATCATACACATCACATCAAGTCATATTCGACTCCCAAACACTAACCAAGCTTCTT--TGCTTCTCAAC-GCTTTGATG") iBioseq3 = Bioseq("MbS67Gr8Cl511 chunk21 {Fragment} 166093..166269", "-GTTTAGCCGAAGTCCATATGAGTCGTTGTGTTTGTATCTTCTAACAAGGAAACACTACTTACGCTTTTAGGATAAGATTGTTGTTTAAGTTCTTATACTTAATCATACACATGACATAAAGTCATATTCGACTCCAAAACACTAATCAAGCTTCTTCTTGCTTCTCAAA-GCTTTGTT-") iBioseq4 = Bioseq("MbS66Gr8Cl511 chunk21 {Fragment} 173353..173529", "--TTTAGCAAAATTCTATATGAGTCTTTATCTTTGTATCTTCTAACAAGGAAACACTACTTAGGCTTTTAGGATAAGGTTGCGGGTTAAGTTCTTATACTCAATCATACACATGATATCAAGTCATATTCGACTCCAAAACACTAACCAAGCTTCTTCTTGCTTCTTAAAAGCTTTGAA-") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expConsensus = Bioseq("consensus= length=178 nbAlign=4 pile=511 pyramid=8", "GTTTAGCCGAAGTCCATATGAGTCTTTGTNTTTGTATCTTCTAACAAGGAAACACTACTTAGGCTTTTAGGATAAGNTTGCNGTTTAAGTTCTTATACTNAATCATACACATGACATCAAGTCATATTCGACTCCAAAACACTAANCAAGCTTCTTCTTGCTTCTCAAAGCTTTGATG") obsConsensus = iAlignedBioseqDB.getConsensus(2, 0.6, isHeaderSAtannot=True) self.assertEquals(expConsensus, obsConsensus) def test_getEntropy_equal_zero(self): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "AGAT") iBioseq3 = Bioseq("seq3", "AGAT") iBioseq4 = Bioseq("seq4", "AGAT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expStats = Stat() expStats._min = 0 expStats._max = 0 expStats._sum = 0 expStats._sumOfSquares = 0 expStats._n = 4 expStats._lValues = [0, 0, 0, 0] obsStats = iAlignedBioseqDB.getEntropy() self.assertEquals(expStats, obsStats) def test_getEntropy_different_nucl(self): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "CTCA") iBioseq3 = Bioseq("seq3", "TTCT") iBioseq4 = Bioseq("seq4", "GTAT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expStats = Stat() expStats._min = 0.81127812445913283 expStats._max = 2.0 expStats._sum = 4.62255624892 expStats._sumOfSquares = 6.31634439045 expStats._n = 4 expStats._lValues = [2.0, 0.81127812445913283, 1.0, 0.81127812445913283] obsStats = iAlignedBioseqDB.getEntropy() self.assertEquals(expStats, obsStats) def test_getEntropy_different_nucl_with_N(self): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "CNCA") iBioseq3 = Bioseq("seq3", "TTNT") iBioseq4 = Bioseq("seq4", "GTNT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expStats = Stat() expStats._min = 0.811278124459 expStats._max = 2 expStats._sum = 6.11387090595 expStats._sumOfSquares = 10.1629200457 expStats._n = 4 expStats._lValues = [2, 1.4913146570363986, 1.8112781244591329, 0.81127812445913283] obsStats = iAlignedBioseqDB.getEntropy() self.assertEquals(expStats, obsStats) def test_getEntropy_different_nucl_with_gap(self): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "C-CA") iBioseq3 = Bioseq("seq3", "T--T") iBioseq4 = Bioseq("seq4", "-TNT") iAlignedBioseqDB = AlignedBioseqDB() iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) expStats = Stat() expStats._min = 0.811278124459 expStats._max = 1.65002242165 expStats._sum = 5.04626304683 expStats._sumOfSquares = 6.89285231586 expStats._n = 4 expStats._lValues = [1.5849625007211561, 1.0, 1.6500224216483541, 0.81127812445913283] obsStats = iAlignedBioseqDB.getEntropy() self.assertEquals(expStats, obsStats) def test_saveAsBinaryMatrix( self ): iBioseq1 = Bioseq("seq1", "AGAT") iBioseq2 = Bioseq("seq2", "C-CA") iBioseq3 = Bioseq("seq3", "T--T") iBioseq4 = Bioseq("seq4", "-TNT") self._i.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4 ] ) expFile = "dummyExpFile_%s" % ( self._uniqId ) expFileHandler = open( expFile, "w" ) expFileHandler.write( "seq1\t1\t1\t1\t1\n" ) expFileHandler.write( "seq2\t1\t0\t1\t1\n" ) expFileHandler.write( "seq3\t1\t0\t0\t1\n" ) expFileHandler.write( "seq4\t0\t1\t1\t1\n" ) expFileHandler.close() obsFile = "dummyObsFile_%s" % ( self._uniqId ) self._i.saveAsBinaryMatrix( obsFile ) self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) for f in [ expFile, obsFile ]: os.remove( f ) def test_getAlignList( self ): iBioseq1 = Bioseq( "seq1", "AGAAT" ) iBioseq2 = Bioseq( "seq2", "-G-AC" ) self._i.setData( [ iBioseq1, iBioseq2 ] ) iAlign1 = Align( Range( "seq1", 2, 2 ), Range( "seq2", 1, 1 ), 0, 1, 100 ) iAlign2 = Align( Range( "seq1", 4, 5 ), Range( "seq2", 2, 3 ), 0, 1, 50 ) lExp = [ iAlign1, iAlign2 ] lObs = self._i.getAlignList( "seq1", "seq2" ) self.assertEquals( lExp, lObs ) def test_removeGaps(self): iBioseq1 = Bioseq( "seq1", "AGAAT-" ) iBioseq2 = Bioseq( "seq2", "AG-ACG" ) self._i.setData( [ iBioseq1, iBioseq2 ] ) exp = AlignedBioseqDB() exp.setData( [ Bioseq( "seq1", "AGAAT" ), Bioseq( "seq2", "AGACG" ) ] ) self._i.removeGaps() self.assertEquals(exp, self._i) def test_computeMeanPcentIdentity_between_two_sequences_50pcent(self): iBioseq1 = Bioseq( "seq1", "AGAAT-" ) iBioseq2 = Bioseq( "seq2", "AG-ACG" ) self._i.setData( [ iBioseq1, iBioseq2 ] ) expIdentity = 50.0 obsIdentity = self._i.computeMeanPcentIdentity() self.assertEquals(expIdentity, obsIdentity) def test_computeMeanPcentIdentity_between_two_sequences_57pcent(self): iBioseq1 = Bioseq( "seq1", "AGAAT-T" ) iBioseq2 = Bioseq( "seq2", "AG-ACGT" ) self._i.setData( [ iBioseq1, iBioseq2 ] ) expIdentity = 57.0 obsIdentity = self._i.computeMeanPcentIdentity() self.assertEquals(expIdentity, obsIdentity) def test_compueNeamPcentIdentity_between_two_sequences_gaps_on_same_position(self): iBioseq1 = Bioseq( "seq1", "AGAAT-T" ) iBioseq2 = Bioseq( "seq2", "AG-AC-T" ) self._i.setData( [ iBioseq1, iBioseq2 ] ) expIdentity = 57.0 obsIdentity = self._i.computeMeanPcentIdentity() self.assertEquals(expIdentity, obsIdentity) def test_computeMeanPcentIdentity_between_three_sequences_50_pcent(self): iBioseqRef = Bioseq( "seqRef", "AGAAT-" ) iBioseq1 = Bioseq( "seq1", "AG-ACG" ) iBioseq2 = Bioseq( "seq2", "AG-ACG" ) self._i.setData( [ iBioseqRef, iBioseq1, iBioseq2 ] ) expIdentity = 50.0 obsIdentity = self._i.computeMeanPcentIdentity() self.assertEquals(expIdentity, obsIdentity) def test_computeMeanPcentIdentity_between_three_sequences_42_pcent(self): iBioseqRef = Bioseq( "seqRef", "AGAAT-" ) iBioseq1 = Bioseq( "seq1", "AG-ACG" ) iBioseq2 = Bioseq( "seq2", "AG-CC-" ) self._i.setData( [ iBioseqRef, iBioseq1, iBioseq2 ] ) expIdentity = 42.0 obsIdentity = self._i.computeMeanPcentIdentity() self.assertEquals(expIdentity, obsIdentity) #TODO: test with tthis data: #>BlastclustCluster2Mb1_chunk7 (dbseq-nr 1) [101523,104351] #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #-------------------------------TAAATCCAACACTGAGAAGAATTATTTAA #AGAAGGTTTTTATTTAACTTCTTTATTCGGATATCAGTTTAAGACTAAAA-TTCA-AATG #TAAATTGGATTGAGGAGAAGCCTCAGTATTTTAACAATATTTGTATTTCGGGAGGGCCTC #GCTTTTGGATTCTTAAGATTAGGAAAAGATTCAAAGAGAGCAGTCAAATCTGCTTATGTC #AGGCTTTAGGATTTTTACAAGAACGGCTAAGTGCCGCTGCCAAAGAATTCTTTATTAGAA #ACGGACGCTGCGCAGCTGGGATACATTATGGAAATAACTTAAGTGCATTACTGTTTTCTT #TGAAATAATTGAAGTGGCCGATTTGGACCACCCAAATACGTACCTCCCCTTCCCTTAAAG #TGAAACCTATACTTGGGCTGGGATTGATAGATATTGTATGGAAAATGGAGTTTGTTCTAT #TTCTATTTGTTGTGGTATGTTTTGATTTTTTCTTATTTTAAGTTTTGCATACAGCAACAT #AA--ATGGCATAA--ATTATACATA-TCTTAAATATAAGTACAATAAAATTAGTCA--AT #TATTACAATGGTCATTAGTATG-TAAAGTGTAAT-ATTGTTCTC-TGA-AATCATCTTAA #CATTGGCGTTGTGTTTTACAATTTTTATTTTTGTTATATTAAGTGGTGTGTCAAGTGGTG #TCAAATCTATTTCTGGTTTTAACATATTTTCACTTAAAATTATACTATTGATTTCTATTT #TGCATTGCATTACTCCTTTCATTTTGTTTTCTTCTATTTTTATATTATTAATTGAATTTG #GGTAATTTTGGTTATGAATGGTTTGGGTTAAGTTCCAGTAATTTGTAATAATTTAAGTTT #AGTAATTTTGGGTTAAACAAGTCAAGTCTGGAAAGCTGGCATAGCCATTCTAAATCTTCT #ACGTATTCCGTAAACTGCATTAGCTAGAACAAAAGTGGTTATTTTCATAGTTCTGTTTTT #TTGGTTTCTTAAGTAAT--TAAT--TTGTATGTTTGATCAAAAAGGGTAACTATTATTTT #TGTAAT--TAATAACTGATTGGACATTTTTCAACAATTTTCTGTCAATTAGCAT----AT #CGTAATTATTAGAA-AATACTATT--TCTGGGTAA-CATAATCAAGTCGTTCAAGGTAAT #AGGGCCATT-TAATGTTAA-AACTTCACTTCTACTATTTTGTATGGGAAGA--CAAAATA #TATTTTCAT--TGATCATATTAATTGTGGAAGCCATTTGTATGTGTACCCTTTGTATACT #ATTTTTAAGCATTCGTGTTGTCCGGGGCTGTTGACCGAAAATTTTCGTTTAGTTCAGAAT #TATTTTGATTTTGTTCATTATTAATGTGTACGGGTTGGACCTGTTGTTGCCCTTCATTAA #TGAACCCATGATTTTGATATGGATTGTATTGATTTTGGTCATAATACTGTTGTTCGTAGG #TTGGGTCTGAAATAATTAGGTACGTGCCACATTGGTGGGTTGTAAGTCGTCTGCTCTGAT #AGCTAGGTCTAAATGGTTGAATGTATTGATTAAAATTAGGCTGGAAGGGTTGGGAATATT #GTGGGTAACTTGGGCGAGTTTGAACGTTTGTATTGAATTTATGTGCTTTCGAATTCTGAT #TAAAATTTGAATTTTTATTACGGTATTCTGGGTTTATAAAATTCAAAATTAATGAGTTTT #TCATAAATTCCCTCATTTTGTGCAATGGTTATTAAGGATCTTAAGTCTGTAATA-TCGTG #ATGAG-ATAA-AATAGTAAATATAGTAG-AGTCTTTA--ATAGCCTGAATAAAAATAAGA #AAATCCGATTGGTTACCTTCCAGGTGTAGTTTCGAAATTAATAATTGACGTCGTCTTTCC #CCTTCTTCGGAGAATGTTTTTAGGTTTCCTCTGTATGGTGTCTCCCTGAAGCTCTCCAGA #AGTTTGTAGTTTGGTGTTTGAGTTTTAAATTCCGCGATGAGTCTTGCTTTGAGGGTAGGC #CAATGCTCGGAAGTCCCAAAGATCGTATTATCCGTCCAAGTTACTTTTGATGGCTCCCAG #TAGAATCCTCTGTTTACGAAAATTACGTAAATCCACTCTGCTGACGACGGTGTGAAGTGT #TTCTGGATCACCCTTAAATGTCATAATGTCTTTAAGCTGCCGACGGGCTTCGGCAAGGTT #GTTGTCTCTTAGCGCAACGATTTAAGGTGCGGCAATAATTATAATAATTGGTTGAGACAT #TTTTATTGTAAAATTTTAAATTTTGTGTTTTATTGTTTTATTGTTTCGAATTCAATGCTA #TTATTTATTTTTTTTTTTGTTTTCTAGTTTCACTTTTTTTTTTATTGTATTGCTTTATTG #TTCTTATTTTATTTTTATATGTTGGTTTTAAAACTTAGTTGCCTTTGGACTTAATGTTTT #TGTTTCGTATTTCACTTCCACTTTAAATTGGATAACAGAATTGGAATTAAAATCCAAGTT #GAAGAGTTTCCACGAATTTATTTGGGAAATGTTTCGAGCACTGGAATCCAGTGACTGGAT #TATAAAATTTAACTTATTTCC-ACTCGAAGGTTCTTTTTT--CGG--------ATACTTT #TTGTATCAGT--TGACTAAGAGCAACACTGAGAAGAATTATTTAAAGAAGGTTTTTATTT #AACTTCTTTATTCGGATATCAGTTTAAGACTAAAA-TTCA-AATGTAAATTGGATTGAGG #AGAAGCCTCAGTATT--TCAACAATATTTGTATT--TCGGGAGGGCCTCGCTCTTGGAT- #-TCTTAAGATTAGGAAAAAATTCA-AAGAGAGCAGTCA-AATC-TGCTTATGTCAGGCTT #TAGGATTTTTACAAGAAGGGC-TAAGTGCCGCTGAAACGGATGC---------------- #------------------------------------------------------------ #------------------------------------------------------------ #------------ #>BlastclustCluster2Mb2_chunk7 (dbseq-nr 1) [99136,100579] #GTAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATA #ATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATA #ATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATC #ATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATA #ATCATAATAATCATAATAATCATAATAATCATAATAATAATAATAATCATAATCATAATC #ATAATAAGCGATAAAAAAATTAAAAAATAAAAATTAAAACCCACTGCAATCACGTTGGAC #GGCGAGTCACAGACGTCAGAATAGTGGTGCGTAAATCCAACGCCGAGAAGAATTACTTCA #AGAAGGTTTTTATTGAACTTCTTTATTCGGATATCAGTTTAAGACTAAAAATTAATAATC #ATAAT---AATCATAATAATCATAATAATCATAATAATCATAATAAT------------- #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #-----------------------------------------------CATA-ATAATCAT #AATAAT--CATAATAATCATA-ATAATCATAATAATCATAATAATCATAATAATCATAAT #AATCATAATAATCATAATAATCATAA----TAATCATAATAATCATAATAATCATAATAA #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------TCATAA-TAATCATAATAATCGTAA---TAATCATAA----TAATCATAATAAT #CATAATAATCATAA-TAAT----CAT-----AATAATCAT-----AATAATCATAATAAT #CATAATAATCATAATAATCATAATAATCATAATAATCATAAT-AA-TCAT--AA--TAAT #-----CATAATAATCATAATAA--TCA----TAATAATC---AT---AATAATCATAATA #-AT---CATAATAATCATAATAATC----------------------------------- #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #-----------------------------------ATAATAATCATAAT-AATCA----- #TAATAA------TCATAAT----AATCATAAT-AATCATAATAA-TCA-TAATAATCATA #ATAATCATAATAATCATAATAATAATAATAATCATAATCATAATCATAATAAGCATAAAA #AAAT-------------------------------------------------------- #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #------------------------------------------------------------ #TAAAAAATAAAAATTAAAACCCACTGCAA---TCACGTTGGACGGCGAGTCACAGACGTC #A-GAAT-AGTGGTGCGTAAATCCAACGCCGAGAAGAATTACTTCAAGAAGGTTTTTATTG #AACTTCTTTATTCGGATATCAGTTTAAGACTAAAAATTAATAATCATAAT---AATCATA #ATAA---TCA-TAATAATCAT-AATAATCATAATAATCATAA-----TAA-TCATA-ATA #ATCATAATAATCATAATAA--TCATAATA-ATCA-TAATAATCATAATAATCATAATCAT #CATAATAATCATAATAAT--CATAA-T-------AATC--ATAATAATCATAATAATCAT #AATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAAT #CATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAAT #AATCATAATAAT test_suite = unittest.TestSuite() test_suite.addTest( unittest.makeSuite( Test_AlignedBioseqDB ) ) if __name__ == "__main__": unittest.TextTestRunner(verbosity=2).run( test_suite )