def test_find_lca_2():
tree = build_tree([[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2a')],
[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2b')],
])
lca = find_lca(tree)
assert lca == ((LineagePair('rank1', 'name1'),), 2)
def test_build_tree_2():
tree = build_tree([[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2a')],
[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2b')],
])
assert tree == { LineagePair('rank1', 'name1'): { LineagePair('rank2', 'name2a') : {},
LineagePair('rank2', 'name2b') : {}} }
def test_build_tree_3(): # empty 'rank2' name
tree = build_tree([[LineagePair('rank1', 'name1'), LineagePair('rank2', '')]])
assert tree == { LineagePair('rank1', 'name1'): {} }
def test_build_tree():
tree = build_tree([[LineagePair('rank1', 'name1'),
LineagePair('rank2', 'name2')]])
assert tree == { LineagePair('rank1', 'name1'):
{ LineagePair('rank2', 'name2') : {}} }
def test_display_lineage_2():
x = [ LineagePair('superkingdom', 'a'), LineagePair(None, ''), LineagePair('class', 'c') ]
assert display_lineage(x) == "a;;c", display_lineage(x)
def test_display_lineage_1():
x = [ LineagePair('superkingdom', 'a'), LineagePair('phylum', 'b') ]
assert display_lineage(x) == "a;b", display_lineage(x)
def test_zip_lineage_4():
x = [ LineagePair('superkingdom', 'a'), LineagePair('class', 'c') ]
with pytest.raises(ValueError) as e:
zip_lineage(x)
assert 'incomplete lineage at phylum - is class instead' in str(e.value)
def test_zip_lineage_3_truncate():
x = [ LineagePair('superkingdom', 'a'), LineagePair(None, ''), LineagePair('class', 'c') ]
assert zip_lineage(x, truncate_empty=True) == ['a', '', 'c']
def test_zip_lineage_3():
x = [ LineagePair('superkingdom', 'a'), LineagePair(None, ''), LineagePair('class', 'c') ]
assert zip_lineage(x) == ['a', '', 'c', '', '', '', '', '']
def test_zip_lineage_2():
x = [ LineagePair('superkingdom', 'a'), LineagePair('phylum', 'b') ]
assert zip_lineage(x, truncate_empty=True) == ['a', 'b']
def test_zip_lineage_1():
x = [ LineagePair('superkingdom', 'a'), LineagePair('phylum', 'b') ]
assert zip_lineage(x) == ['a', 'b', '', '', '', '', '', '']
def test_find_lca():
tree = build_tree([[LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2')]])
lca = find_lca(tree)
assert lca == ((LineagePair('rank1', 'name1'), LineagePair('rank2', 'name2'),), 0)