def setUp(self): CWD = os.getcwd() data_dir = path_utils.get_data_dir(CWD) self.Blast_dir = data_dir + "BLAST/" self.infile = data_dir + "AE014075_subTiny5.fasta" # "AE014075_subSmall100.fasta" self.e_threshold = 1e-15 self.record_index = SeqIO.index(self.infile, "fasta") self.template_set = dict({ 'S1': set([]), 'S2': set(['GO:01', 'GO:02']), 'S3': set(['GO:01', 'GO:03', 'GO:04']), 'S4': set(['GO:03', 'GO:04', 'GO:05']), 'S5': set(['GO:01', 'GO:05', 'GO:06', 'GO:07']), }) self.template_set_small = dict({ 'S3': set(['GO:01', 'GO:03', 'GO:04']), 'S4': set(['GO:03', 'GO:04', 'GO:05']), }) self.S1 = self.template_set.get("S1") self.S2 = self.template_set.get("S2") self.S3 = self.template_set.get("S3") self.S4 = self.template_set.get("S4") self.S5 = self.template_set.get("S5")
def setUp(self): """ TODO: add wdir section """ self.maxDiff = None self.long_message = True self.data_dir = path_utils.get_data_dir() + "Glimmer/"
def setUp(self): datadir = get_data_dir() self.infile = datadir + "test.fasta" self.outfile = datadir + "test_temp.txt" # args = parser.parse_args(["-h"]) self.BLAST = runBLAST(self.infile, self.outfile)
def setUp(self): self.maxDiff = None self.unittest_dir = path_utils.get_data_dir() + "unittest_data/" self.genovo_dir = path_utils.get_data_dir() + "Genovo/" self.glimmer_dir = path_utils.get_data_dir() + "Glimmer/" self.metasim_dir = path_utils.get_data_dir() + "MetaSim/" self.mine_dir = path_utils.get_data_dir() + "MINE/" self.blast_dir = path_utils.get_data_dir() + "BLAST/" self.working_dir = path_utils.get_data_dir() + "test_data/"
def setUp(self): self.data_dir = path_utils.get_data_dir() + "/unittest_data/"
def setUp(self): CWD = os.getcwd() self.data_dir = path_utils.get_data_dir(CWD) infile = self.data_dir + "AE014075_subTiny10.fasta" # "AE014075_subSmall100.fasta" self.e_threshold = 1e-15 self.record_index = SeqIO.index(infile, "fasta")
def setUp(self): self.longMessage = True self.data_dir = path_utils.get_data_dir() + "unittest_data/" self.wdir = path_utils.get_data_dir() + "Genovo/test_data/"
def setUp(self): self.long_message = True self.data_dir = path_utils.get_data_dir() + "MINE/" self.working_dir = path_utils.get_data_dir() + "MINE/test_data/"
def setUp(self): self.data_dir = path_utils.get_data_dir() + "unittest_data/" self.wdir = "working_dir" self.maxDiff = None