Mercurial > repos > yufei-luo > s_mart
view commons/core/sql/test/Test_TableSeqAdaptator.py @ 13:03045debed6e
Uploaded
author | m-zytnicki |
---|---|
date | Wed, 17 Apr 2013 10:39:35 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
# 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 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 )