annotate commons/core/sql/test/Test_TableSeqAdaptator.py @ 6:769e306b7933

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# Copyright INRA (Institut National de la Recherche Agronomique)
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import unittest
import os
import time
from commons.core.sql.DbMySql import DbMySql
from commons.core.sql.TableSeqAdaptator import TableSeqAdaptator
from commons.core.seq.Bioseq import Bioseq
from commons.core.coord.Set import Set
from commons.core.utils.FileUtils import FileUtils


class Test_TableSeqAdaptator( unittest.TestCase ):
    
    def setUp( self ):
        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
        self.fileUtils = FileUtils()
        self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
        configF = open(self._configFileName, "w" )
        configF.write( "[repet_env]\n" )
        configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
        configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
        configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
        configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
        configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
        configF.close()
        self._db = DbMySql( cfgFileName=self._configFileName )
        self._table = "dummySeqTable_%s" % ( self._uniqId )
        self._tsA = TableSeqAdaptator( self._db, self._table )
        
        
    def tearDown( self ):
        self._db.dropTable( self._table )
        self._db.close()
        os.remove( self._configFileName )
        self._configFileName = ""
        
        
##################################################################################
################## Tests for methods in ITableSeqAdaptator #######################
##################################################################################
        
    def test_insert( self ):
        bs = Bioseq( "seq1", "AGCGATGACGATGCGAGT" )
        self._db.createTable( self._table, "fasta" )
        self._tsA.insert( bs )
        
        expBioseqTuple = (("seq1", "AGCGATGACGATGCGAGT", "seq1", 18L), )
        
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._db.execute( sqlCmd )
        obsBioseqTuple = self._db.cursor.fetchall()
        
        self.assertEqual( expBioseqTuple, obsBioseqTuple )
        
        
    def test_insertList( self ):
        bs1 = Bioseq( "seq1 desc", "AGCGATGACGATGCGAGT" )
        bs2 = Bioseq( "seq2", "AGCGATGACGATGCGAGT")
        bs3 = Bioseq( "seq3", "GCGATGCAGATGACGGCGGATGC")
        lBioseq = [ bs1, bs2, bs3 ]
        self._db.createTable( self._table, "fasta" )
        self._tsA.insertList( lBioseq )
        
        tuple1 = ("seq1", "AGCGATGACGATGCGAGT", "seq1 desc", 18L)
        tuple2 = ("seq2", "AGCGATGACGATGCGAGT", "seq2", 18L)
        tuple3 = ("seq3", "GCGATGCAGATGACGGCGGATGC", "seq3", 23L)
        expBioseqTuple = ( tuple1, tuple2, tuple3 )
        
        sqlCmd = "SELECT * FROM %s" % ( self._table )
        self._db.execute( sqlCmd )
        obsBioseqTuple = self._db.cursor.fetchall()
        
        self.assertEquals(expBioseqTuple, obsBioseqTuple)
        
        
    def test_getAccessionsList(self):
        faFileName = "dummyFaFile_%s" % ( self._uniqId )
        faF = open( faFileName, "w" )
        faF.write(">seq1\n")
        faF.write("AGCGATGACGATGCGAGT\n")
        faF.write(">seq2\n")
        faF.write("GCGATGCAGATGACGGCGGATGC\n")
        faF.close()
        self._db.createTable( self._table, "fasta", faFileName )
        lExp = [ "seq1", "seq2" ]
        lExp.sort()
        lObs = self._tsA.getAccessionsList()
        lObs.sort()
        self.assertEqual( lObs, lExp )
        os.remove( faFileName )
        
        
    def test_saveAccessionsListInFastaFile(self):
        expFileName = "dummyFaFile_%s" % ( self._uniqId )
        expF = open( expFileName, "w" )
        expF.write(">seq1\n")
        expF.write("AGCGATGACGATGCGAGT\n")
        expF.write(">seq2\n")
        expF.write("GCGATGCAGATGACGGCGGATGC\n")
        expF.close()
        self._db.createTable( self._table, "fasta", expFileName )
        lAccessions = [ "seq1", "seq2" ]
        obsFileName = "dummyObsFile_%s" % ( self._uniqId )
        self._tsA.saveAccessionsListInFastaFile( lAccessions, obsFileName )
        self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
        os.remove( expFileName )
        os.remove( obsFileName )
        
    def test_exportInFastaFile(self):
        expFileName = "dummyFaFile_%s" % ( self._uniqId )
        faF = open( expFileName, "w" )
        faF.write(">seq1\n")
        faF.write("AGCGATGACGATGCGAGT\n")
        faF.write(">seq2\n")
        faF.write("GCGATGCAGATGACGGCGGATGC\n")
        faF.close()
        self._db.createTable( self._table, "fasta", expFileName )
        obsFileName = "dummyFaFileObs_%s" % ( self._uniqId )
        self._tsA.exportInFastaFile( obsFileName )
        self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
        os.remove( expFileName )
        os.remove( obsFileName )

##################################################################################
########################### Tests for other methods ##############################
##################################################################################
        
    def test_insertWithBioseqEmpty( self ):
        bs = Bioseq( "", "" )
        self._db.createTable( self._table, "fasta" )
        exp = None
        obs = self._tsA.insert(bs)
        self.assertEqual( exp, obs )
        
        
    def test_getBioseqFromHeader( self ):
        faFileName = "dummyFaFile_%s" % ( self._uniqId )
        faF = open( faFileName, "w" )
        faF.write(">seq1\n")
        faF.write("AGCGATGACGATGCGAGT\n")
        faF.write(">seq2\n")
        faF.write("GCGATGCAGATGACGGCGGATGC\n")
        faF.close()
        self._db.createTable( self._table, "fasta", faFileName )
        exp = Bioseq( "seq1", "AGCGATGACGATGCGAGT" )
        obs = self._tsA.getBioseqFromHeader( "seq1" )
        self.assertEqual( obs, exp )
        exp = Bioseq( "seq2", "GCGATGCAGATGACGGCGGATGC" )
        obs = self._tsA.getBioseqFromHeader( "seq2" )
        self.assertEqual( obs, exp )
        os.remove( faFileName )
        
        
    def test_getSeqLengthFromAccession( self ):
        inFileName = "dummyFaFile_%s" % ( self._uniqId )
        inF = open( inFileName, "w" )
        inF.write(">seq1\n")
        inF.write("AGCGATGACGATGCGAGT\n")
        inF.write(">seq2\n")
        inF.write("GCGATGCAGATGACGGCGGATGC\n")
        inF.close()
        self._db.createTable( self._table, "fasta", inFileName )
        exp = 18
        obs = self._tsA.getSeqLengthFromAccession( "seq1" )
        self.assertEqual( obs, exp )
        os.remove( inFileName )


    def test_getSeqLengthFromDescription( self ):
        inFileName = "dummyFaFile_%s" % ( self._uniqId )
        inF = open( inFileName, "w" )
        inF.write(">seq1 descriptionfield\n")
        inF.write("AGCGATGACGATGCGAGT\n")
        inF.write(">seq2 descriptionfield\n")
        inF.write("GCGATGCAGATGACGGCGGATGC\n")
        inF.close()
        self._db.createTable( self._table, "fasta", inFileName )
        exp = 18
        obs = self._tsA.getSeqLengthFromDescription( "seq1 descriptionfield" )
        self.assertEqual( obs, exp )
        os.remove( inFileName )
        
        
    def test_getAccessionAndLengthList( self ):
        inFileName = "dummyFaFile_%s" % ( self._uniqId )
        inF = open( inFileName, "w" )
        inF.write(">seq1\n")
        inF.write("AGCGATGACGATGCGAGT\n")
        inF.write(">seq2\n")
        inF.write("GCGATGCAGATGACGGCGGATGC\n")
        inF.close()
        self._db.createTable( self._table, "fasta", inFileName )
        lSeq1 = ("seq1", 18)
        lSeq2 = ("seq2", 23)
        lExp = [lSeq1,lSeq2]
        lObs = self._tsA.getAccessionAndLengthList()
        self.assertEqual( lObs, lExp )
        os.remove( inFileName )
        
        
    def test_getSeqLengthFromAccessionWithSingleQuote( self ):
        inFileName = "dummyFaFile_%s" % ( self._uniqId )
        inF = open( inFileName, "w" )
        inF.write(">seq1'\n")
        inF.write("AGCGATGACGATGCGAGT\n")
        inF.write(">seq2\n")
        inF.write("GCGATGCAGATGACGGCGGATGC\n")
        inF.close()
        self._db.createTable( self._table, "fasta", inFileName )
        exp = 18
        obs = self._tsA.getSeqLengthFromAccession( "seq1'" )
        self.assertEqual( obs, exp )
        os.remove( inFileName )
        
        
    def test_getSubSequence_directStrand( self ):
        self._db.createTable( self._table, "seq" )
        chr = Bioseq()
        chr.setHeader( "chr2" )
        chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
        self._tsA.insert( chr )
        exp = "TTTGGG"
        obs = self._tsA.getSubSequence( "chr2", 13, 18 )
        self.assertEqual( exp, obs )
        
        
    def test_getSubSequence_reverseStrand( self ):
        self._db.createTable( self._table, "seq" )
        chr = Bioseq()
        chr.setHeader( "chr2" )
        chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
        self._tsA.insert( chr )
        exp = "CCCAAA"
        obs = self._tsA.getSubSequence( "chr2", 18, 13 )
        self.assertEqual( exp, obs )
        
        
    def test_getBioseqFromSetList_directStrand( self ):
        self._db.createTable( self._table, "seq" )
        chr = Bioseq()
        chr.setHeader( "chr2" )
        chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
        self._tsA.insert( chr )
        lSets = []
        lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 1, 10 ) )
        lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 16, 25 ) )
        exp = Bioseq( "Dm-B-G600-Map3_classI-LTR-incomp::3 chr2 1..10,16..25", "AAAAAAAAAAGGGGGGGGGG" )
        obs = self._tsA.getBioseqFromSetList( lSets )
        self.assertEqual( exp, obs )
        
        
    def test_getBioseqFromSetList_reverseStrand( self ):
        self._db.createTable( self._table, "seq" )
        chr = Bioseq()
        chr.setHeader( "chr2" )
        chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
        self._tsA.insert( chr )
        lSets = []
        lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 10, 1 ) )
        lSets.append( Set( 3, "Dm-B-G600-Map3_classI-LTR-incomp", "chr2", 25, 16 ) )
        exp = Bioseq( "Dm-B-G600-Map3_classI-LTR-incomp::3 chr2 25..16,10..1", "CCCCCCCCCCTTTTTTTTTT" )
        obs = self._tsA.getBioseqFromSetList( lSets )
        self.assertEqual( exp, obs )
        
        
    def test_isAccessionInTable_true( self ):
        self._db.createTable( self._table, "seq" )
        chr = Bioseq()
        chr.setHeader( "chr2" )
        chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
        self._tsA.insert( chr )
        
        obs = self._tsA.isAccessionInTable( "chr2" )
        self.assertTrue( obs )
        
        
    def test_isAccessionInTable_false( self ):
        self._db.createTable( self._table, "seq" )
        chr = Bioseq()
        chr.setHeader( "chr2" )
        chr.setSequence( "AAAAAAAAAATTTTTGGGGGGGGGG" )
        self._tsA.insert( chr )
        
        obs = self._tsA.isAccessionInTable( "chr1" )
        self.assertFalse( obs )
        
        
test_suite = unittest.TestSuite()
test_suite.addTest( unittest.makeSuite( Test_TableSeqAdaptator ) )
if __name__ == "__main__":
    unittest.TextTestRunner(verbosity=2).run( test_suite )