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)