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():
# 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 test_choose_1(self):
'''
Ensure choose can handle when Chdb is not present, running checkM automatically
'''
# Delete Chdb
wd_loc = self.working_wd_loc
os.remove(wd_loc + '/data_tables/Chdb.csv')
# Modify Bdb so the genome locations are right
genomes = test_utils.load_test_genomes()
g2l = {os.path.basename(g): g for g in genomes}
Bdb = pd.read_csv(wd_loc + '/data_tables/Bdb.csv')
Bdb['location'] = Bdb['genome'].map(g2l)
Bdb.to_csv(wd_loc + '/data_tables/Bdb.csv', index=False)
# Run choose - this should re-run checkM and re-generate chdb
drep.d_choose.d_choose_wrapper(wd_loc, checkM_method='taxonomy_wf')
# args = argumentParser.parse_args(['choose', wd_loc, '--checkM_method', \
# 'taxonomy_wf'])
# controller = Controller()
# controller.parseArguments(args)
Swd = WorkDirectory(self.s_wd_loc)
wd = WorkDirectory(self.working_wd_loc)
for db in ['Chdb', 'genomeInformation']:
db1 = Swd.get_db(db)
db2 = wd.get_db(db)
assert test_utils.compare_dfs(db1,
db2), "{0} is not the same!".format(db)
def test_n50(self):
'''
test N50 calculation
'''
import drep.d_filter
genomes = test_utils.load_test_genomes()
# test a genome with a single scaffold
genome = [x for x in genomes if 'EC20' in x][0]
n50 = drep.d_filter.calc_n50(genome)
assert n50 == 3427276
# test a real genome
genome = [x for x in genomes if 'T2' in x][0]
n50 = drep.d_filter.calc_n50(genome)
assert n50 == 774663, n50
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(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.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 self():
# Set up
self = Empty()
self.genomes = test_utils.load_test_genomes()
self.wd_loc = test_utils.load_test_wd_loc()
if os.path.isdir(self.wd_loc):
shutil.rmtree(self.wd_loc)
self.s_wd_loc = test_utils.load_solutions_taxonomy_wd()
# copy over the data from solutions directory
os.mkdir(self.wd_loc)
shutil.copytree(os.path.join(self.s_wd_loc, 'data'), \
os.path.join(self.wd_loc, 'data'))
importlib.reload(logging)
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.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)
