Exemple #1
0
    def setUp(self):
        
        self.buf = open('data/ProtDNA.psl').read()
        self.buf = self.buf.replace("\r\n","\n")

        thisdir = os.path.abspath(os.path.dirname(__file__))
        def thisfile(name):
            return os.path.join(thisdir, name)
        
        
        self.srcDB = seqdb.SequenceFileDB(thisfile('data/test_prot.fa'))
        self.destDB = seqdb.SequenceFileDB(thisfile('data/test_dna.fa'))
        self.db = seqdb.SequenceFileDB(thisfile('data/translatedDB.fa'))
        
        self.aln_type = 1 #protein-dna alignmet = 1, else - 0 
        
        self.matches, genome_names = blat_NLMSA.parse_blat(self.buf, 
                                                           self.aln_type)

        self.db = translationDB.get_translation_db(self.destDB)

        alignment = cnestedlist.NLMSA('test', mode='memory', pairwiseMode=True,
                                      bidirectional=False)

        self.temp_nlmsa = blat_NLMSA.create_NLMSA_blat(self.buf, alignment,
                                                       aln_type = self.aln_type,        
                                                       srcDB = self.srcDB, 
                                                       destDB = self.db)
Exemple #2
0
    def setUp(self):
        self.buf = open('data/output.psl').read()
        self.buf = self.buf.replace("\r\n","\n")
        
        thisdir = os.path.abspath(os.path.dirname(__file__))
        self.db = seqdb.SequenceFileDB(os.path.join(thisdir,
                                                    'data/test_genomes.fna'))
        self.aln_type = 0 #if protein-dna-1,else-0      
        matches, genome_names = blat_NLMSA.parse_blat(self.buf, self.aln_type)
        
        alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.db,
                                      use_virtual_lpo=True)

        self.temp_nlmsa = blat_NLMSA.create_NLMSA_blat(self.buf, alignment,
                                                       seqDB=self.db)
    def setUp(self):
        self.buf = open('data/output.psl').read()
        self.buf = self.buf.replace("\r\n","\n")
        
        thisdir = os.path.abspath(os.path.dirname(__file__))
        
        def thisfile(name):
            return os.path.join(thisdir, name)

        self.srcDB = seqdb.SequenceFileDB(thisfile('data/test_genomes.fna'))
        self.destDB = seqdb.SequenceFileDB(thisfile('data/test_genomes.fna'))
        
        self.protDNAaln = False #if protein-dna alignment - True,else- False      
       
        matches, genome_names = blat_NLMSA.parse_blat(self.buf, self.protDNAaln)
        
        alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.srcDB,
                                     use_virtual_lpo=True)
        #alignment = cnestedlist.NLMSA('test', mode='memory', pairwiseMode=True,
                                      #bidirectional=False)????????

        self.temp_nlmsa = blat_NLMSA.create_NLMSA_blat(self.buf, alignment,
                                                       self.srcDB, self.destDB,
                                                       self.protDNAaln)