def self():
# Set up
self = Empty()
self.genomes = test_utils.load_test_genomes()
self.broken_genome = test_utils.load_broken_genome()
self.wd_loc = test_utils.load_test_wd_loc()
self.test_dir = test_utils.load_random_test_dir()
self.s_wd_loc = test_utils.load_solutions_wd()
if os.path.isdir(self.test_dir):
shutil.rmtree(self.test_dir)
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc, ignore_errors=True)
if not os.path.isdir(self.test_dir):
os.mkdir(self.test_dir)
importlib.reload(logging)
yield self
# Teardown
logging.shutdown()
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
if os.path.isdir(self.test_dir):
shutil.rmtree(self.test_dir)
def self():
# Set up
self = Empty()
self.s_wd_loc = test_utils.load_solutions_wd()
self.working_wd_loc = test_utils.load_test_wd_loc()
self.genomes = test_utils.load_test_genomes()
logging.shutdown()
if os.path.isdir(self.working_wd_loc):
shutil.rmtree(self.working_wd_loc, ignore_errors=True)
os.mkdir(self.working_wd_loc)
shutil.copytree(os.path.join(self.s_wd_loc, 'data'), \
os.path.join(self.working_wd_loc, 'data'))
shutil.rmtree(os.path.join(self.working_wd_loc, 'data',
'Clustering_files'))
importlib.reload(logging)
yield self
# Teardown
logging.shutdown()
if os.path.isdir(self.working_wd_loc):
shutil.rmtree(self.working_wd_loc, ignore_errors=True)
def self(caplog):
# Set up
self = Empty()
self._caplog = caplog
self.genomes = test_utils.load_test_genomes()
self.wd_loc = test_utils.load_test_wd_loc()
self.s_wd_loc = test_utils.load_solutions_wd()
self.testdir = test_utils.load_random_test_dir()
self.stinker_genome = os.path.join(test_utils.load_test_backend(), 'other/Enterococcus_faecalis_TX0104.fa')
self.prodigal_loc = os.path.join(test_utils.load_solutions_wd(), 'data/prodigal/')
# Teardown
importlib.reload(logging)
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
yield self
def self():
# Set up
self = Empty()
self.genomes = test_utils.load_test_genomes()
self.wd_loc = test_utils.load_test_wd_loc()
self.s_wd_loc = test_utils.load_solutions_wd()
self.testdir = test_utils.load_random_test_dir()
importlib.reload(logging)
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
yield self
# Teardown
logging.shutdown()
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
def self():
# Set up
self = Empty()
self.genomes = test_utils.load_test_genomes()
self.wd_loc = test_utils.load_test_wd_loc()
self.s_wd_loc = test_utils.load_solutions_wd()
self.zipped_genome = test_utils.load_zipped_genome()
importlib.reload(logging)
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
os.mkdir(self.wd_loc)
yield self
importlib.reload(logging)
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
os.mkdir(self.wd_loc)
def test_goANI2(self):
'''
Test goANI in the case where the genomes share no genes
'''
import time
bdb = drep.d_cluster.utils.load_genomes(self.genomes)
data_folder = self.test_dir
# Copy over prodigal
self.s_wd_loc = test_utils.load_solutions_wd()
p_folder = os.path.join(data_folder, 'data/prodigal/')
shutil.copytree(os.path.join(self.s_wd_loc, 'data/prodigal'), \
p_folder)
# Remove all but one gene in one of the prodigal files
p_folder = os.path.join(data_folder, 'data/prodigal/')
for f in glob.glob(p_folder + '*'):
if 'Escherichia_coli_Sakai.fna.fna' in f:
new_file = open(f + '.2', 'w')
old_file = open(f, 'r')
j = 0
for line in old_file.readlines():
if ((line[0] == '>') & (j != 0)):
break
j += 1
new_file.write(line.strip() + '/')
new_file.close()
old_file.close()
os.remove(f)
shutil.copy(f + '.2', f)
# Try goANI
p_folder = os.path.join(data_folder, 'data/prodigal/')
Ndb = drep.d_cluster.compare_utils.compare_genomes(bdb, 'goANI', data_folder, \
prod_folder = p_folder)
db = Ndb[(Ndb['reference'] == 'Enterococcus_faecalis_T2.fna')\
& (Ndb['querry'] == 'Enterococcus_casseliflavus_EC20.fasta')]
assert (db['ani'].tolist()[0] > 0.7) & (db['ani'].tolist()[0] < 0.8)
def test_goANI(self):
'''
Test goANI
'''
import time
bdb = drep.d_cluster.utils.load_genomes(self.genomes)
data_folder = self.test_dir
# Copy over prodigal
self.s_wd_loc = test_utils.load_solutions_wd()
p_folder = os.path.join(data_folder, 'data/prodigal/')
shutil.copytree(os.path.join(self.s_wd_loc, 'data/prodigal'), \
p_folder)
# Try goANI
p_folder = os.path.join(data_folder, 'data/prodigal/')
Ndb = drep.d_cluster.compare_utils.compare_genomes(bdb, 'goANI', data_folder, \
prod_folder = p_folder)
db = Ndb[(Ndb['reference'] == 'Enterococcus_faecalis_T2.fna')\
& (Ndb['querry'] == 'Enterococcus_casseliflavus_EC20.fasta')]
assert (db['ani'].tolist()[0] > 0.7) & (db['ani'].tolist()[0] < 0.8)
def self():
# Set up
self = Empty()
self.genomes = test_utils.load_test_genomes()
self.zipped_genomes = test_utils.load_zipped_genomes()
self.large_genome_set = test_utils.load_large_genome_set()
self.wd_loc = test_utils.load_test_wd_loc()
self.wd_loc2 = test_utils.load_test_wd_loc_2()
self.s_wd_loc = test_utils.load_solutions_wd()
importlib.reload(logging)
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
if os.path.isdir(self.wd_loc2):
shutil.rmtree(self.wd_loc2)
yield self
# Teardown
logging.shutdown()
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
if os.path.isdir(self.wd_loc2):
shutil.rmtree(self.wd_loc2)