annotate smart_toolShed/commons/core/seq/test/Test_AlignedBioseqDB.py @ 0:e0f8dcca02ed

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

# 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 )