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_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))
class TaxTreeHelperTests(unittest.TestCase):
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 tearDown(self):
self.taxonomy = None
self.taxtree_helper = None
def test_outgroup(self):
mfu_tree_fname = os.path.join(self.testfile_dir, "taxtree.nw")
mfu_tree = Tree(mfu_tree_fname)
self.taxtree_helper.set_mf_rooted_tree(mfu_tree)
outgr = self.taxtree_helper.get_outgroup()
self.assertEqual(outgr.get_leaf_names(),
self.expected_outgr.get_leaf_names())
def test_branch_labeling(self):
bfu_tree_fname = os.path.join(self.testfile_dir, "resolved_tree.nw")
bfu_tree = Tree(bfu_tree_fname)
map_fname = os.path.join(self.testfile_dir, "bid_tax_map.txt")
self.expected_map = {}
with open(map_fname) as inf:
for line in inf:
bid, rank_id, rdiff, brlen = line.strip().split("\t")
self.expected_map[bid] = (rank_id, int(rdiff), float(brlen))
self.taxtree_helper.set_outgroup(self.expected_outgr)
self.taxtree_helper.set_bf_unrooted_tree(bfu_tree)
bid_tax_map = self.taxtree_helper.get_bid_taxonomy_map()
self.assertEqual(len(bid_tax_map), 2 * len(bfu_tree) - 3)
for bid in self.expected_map.iterkeys():
e_rec = self.expected_map[bid]
rec = bid_tax_map[bid]
self.assertEqual(e_rec[0], rec[0])
self.assertEqual(e_rec[1], rec[1])
self.assertAlmostEqual(e_rec[2], rec[2], 6)
class TaxTreeHelperTests(unittest.TestCase):
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 tearDown(self):
self.taxonomy = None
self.taxtree_helper = None
def test_outgroup(self):
mfu_tree_fname = os.path.join(self.testfile_dir, "taxtree.nw")
mfu_tree = Tree(mfu_tree_fname)
self.taxtree_helper.set_mf_rooted_tree(mfu_tree)
outgr = self.taxtree_helper.get_outgroup()
self.assertEqual(outgr.get_leaf_names(), self.expected_outgr.get_leaf_names())
def test_branch_labeling(self):
bfu_tree_fname = os.path.join(self.testfile_dir, "resolved_tree.nw")
bfu_tree = Tree(bfu_tree_fname)
map_fname = os.path.join(self.testfile_dir, "bid_tax_map.txt")
self.expected_map = {}
with open(map_fname) as inf:
for line in inf:
bid, rank_id, rdiff, brlen = line.strip().split("\t")
self.expected_map[bid] = (rank_id, int(rdiff), float(brlen))
self.taxtree_helper.set_outgroup(self.expected_outgr)
self.taxtree_helper.set_bf_unrooted_tree(bfu_tree)
bid_tax_map = self.taxtree_helper.get_bid_taxonomy_map()
self.assertEqual(len(bid_tax_map), 2 * len(bfu_tree) - 3)
for bid in self.expected_map.iterkeys():
e_rec = self.expected_map[bid]
rec = bid_tax_map[bid]
self.assertEqual(e_rec[0], rec[0])
self.assertEqual(e_rec[1], rec[1])
self.assertAlmostEqual(e_rec[2], rec[2], 6)
