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)
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)