def test_tree_integrity_ascii(self):
with open('test_data/tree_example.p', 'rb') as file:
test_tree = pickle.load(file)
TaxTree.ranked_lineage_filepath = '../../bin/database/taxonomy/rankedlineage.dmp'
rootNode = TaxTree.TaxNode("ROOT")
TaxTree.loadRankedLineage(species_indexes,rootNode)
rootNode.countChildren()
ETETree = TaxTree.create_ETE_tree(rootNode)
ascii = TaxTree.get_ASCII_tree(ETETree)
self.assertEqual(ascii, test_tree)
def test_least(self):
with open('test_data/least_example.p', 'rb') as file:
least_test = pickle.load(file)
TaxTree.ranked_lineage_filepath = '../../bin/database/taxonomy/rankedlineage.dmp'
rootNode = TaxTree.TaxNode("ROOT")
TaxTree.loadRankedLineage(species_indexes, rootNode)
rootNode.countChildren()
ranks = ['Species', 'Genus', 'Family', 'Order',
'Class', 'Phylum', 'Kingdom', 'Superkingdom', 'All']
f = io.StringIO()
with redirect_stdout(f):
for r in ranks:
rootNode.calculateCommonnessByRank(r, 5, rootNode, False)
output = f.getvalue()
self.assertEqual(least_test, output)
def test_ETETree(self):
with open('test_data/ETETree_example.p', 'rb') as file:
ETETree_example = pickle.load(file)
TaxTree.ranked_lineage_filepath = '../../bin/database/taxonomy/rankedlineage.dmp'
rootNode = TaxTree.TaxNode("ROOT")
TaxTree.loadRankedLineage(species_indexes, rootNode)
rootNode.countChildren()
ETETree = TaxTree.create_ETE_tree(rootNode)
f = io.StringIO()
with redirect_stdout(f):
ETETree.describe()
ETE_describe = f.getvalue()
t = io.StringIO()
with redirect_stdout(t):
ETETree_example.describe()
ETE_test_describe = t.getvalue()
self.assertEqual(ETE_describe,ETE_test_describe)