def setUp(self):
self.testfile_dir = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "testfiles")
self.tax_fname = os.path.join(self.testfile_dir, "test_clean.tax")
self.taxonomy = Taxonomy(EpacConfig.REF_SEQ_PREFIX, self.tax_fname)
tax_map = self.taxonomy.get_map()
cfg = EpacConfig()
self.taxtree_helper = TaxTreeHelper(cfg, tax_map)
outgr_fname = os.path.join(self.testfile_dir, "outgroup.nw")
self.expected_outgr = Tree(outgr_fname)
def test_taxtree_builder(self):
cfg = EpacConfig()
testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testfiles")
tax_fname = os.path.join(testfile_dir, "test.tax")
tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname)
tree_fname = os.path.join(testfile_dir, "taxtree.nw")
expected_tree = Tree(tree_fname, format=8)
tb = TaxTreeBuilder(cfg, tax)
tax_tree, seq_ids = tb.build()
self.assertEqual(seq_ids, tax.get_map().keys())
self.assertEqual(tax_tree.write(format=8), expected_tree.write(format=8))
def test_epac_config(self):
args = self.get_default_namespace()
cfg = EpacConfig(args)
self.check_common_config(cfg)
def setUp(self):
self.cfg = EpacConfig()
self.testfile_dir = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "testfiles")
