def setUp(self):
self.buf = open('output').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,
'test_genomes.fna'))
matches, genome_names = blastz_NLMSA.parse_blastz(self.buf)
alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.db,
use_virtual_lpo=True)
self.temp_nlmsa = blastz_NLMSA.create_NLMSA_blastz(self.buf,
self.db, alignment)
def setUp(self):
self.buf = open('output').read()
thisdir = os.path.abspath(os.path.dirname(__file__))
self.db = seqdb.SequenceFileDB(os.path.join(thisdir,
'test_genomes.fna'))
matches, genome_names = blastz_NLMSA.parse_blastz(self.buf)
genomes_dict = {}
for genome in genome_names:
genomes_dict[genome] = self.db[genome]
alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.db,
use_virtual_lpo=True)
alignment += genomes_dict[genome_names[0]]
self.temp_nlmsa = blastz_NLMSA.create_NLMSA_blastz(os.path.join(thisdir, 'output'),
self.db, alignment)
def setUp(self):
self.buf = open("output").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.db = seqdb.SequenceFileDB(thisfile("test_genomes.fna"))
matches, genome_names = blastz_NLMSA.parse_blastz(self.buf)
alignment = cnestedlist.NLMSA("test", mode="memory", seqDict=self.db, use_virtual_lpo=True)
self.temp_nlmsa = blastz_NLMSA.create_NLMSA_blastz(self.buf, self.db, alignment)