def setUp(self):
"""
Initilize/create the NLMSA using : .aln alignment file,
the file containing the genomes created with in memory mode,
read in the sequences from the genomes file
"""
thisdir = os.path.abspath(os.path.dirname(__file__))
def thisfile(name):
return os.path.join(thisdir, name)
self.db = seqdb.SequenceFileDB(thisfile('test_genomes_file'))
buf = open(thisfile('test_clustalw_alignment.aln'), "r").read()
clustal_res_list = Clustalw_NLMSA.read_clustalw(buf.split("\n"))
alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.db,
use_virtual_lpo=True)
self.temp_nlmsa = Clustalw_NLMSA.create_NLMSA_clustalw(buf, self.db,
alignment)
def setUp(self):
"""
Initialize the residues from a test file
"""
thisdir = os.path.abspath(os.path.dirname(__file__))
self.db = seqdb.SequenceFileDB(os.path.join(thisdir,
'test_genomes_file'))
lines = open(os.path.join(thisdir, 'test_clustalw_alignment.aln')).readlines()
self.clustalw_resds = Clustalw_NLMSA.read_clustalw(lines)
def setUp(self):
#initilize/create the NLMSA using : .aln alignment file,
#the file containing the genomes created with in memory mode,
#read in the sequences from the genomes file
thisdir = os.path.abspath(os.path.dirname(__file__))
self.db = seqdb.SequenceFileDB(os.path.join(thisdir,
'test_genomes_file'))
clustal_res_list = Clustalw_NLMSA.read_clustalw('test_clustalw_alignment.aln')
genome_names = clustal_res_list[0].get_names()
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 = Clustalw_NLMSA.create_NLMSA_clustalw('test_clustalw_alignment.aln',self.db,alignment)
def setUp(self):
#initialize the residues from a test file
self.clustalw_resds = Clustalw_NLMSA.read_clustalw('test_clustalw_alignment.aln')