def testCandidates(self):
tree = '((((HUMAN:0.006969,CHIMP:0.009727)Anc7:0.025291,BABOON:0.044568)Anc6:0.11,(MOUSE:0.072818,RAT:0.081244)Anc5:0.260342)Anc4:0.023260,((DOG:0.07,CAT:0.07)Anc3:0.087381,(PIG:0.06,COW:0.06)Anc2:0.104728)Anc1:0.04)Anc0;'
mcTree = MultiCactusTree(NXNewick().parseString(tree, addImpliedRoots = False))
mcTree.computeSubtreeRoots()
og = GreedyOutgroup()
og.importTree(mcTree)
candidates = set(['HUMAN', 'CHIMP', 'RAT'])
og.greedy(candidateSet=candidates, candidateChildFrac=0.5)
assert og.ogMap['Anc1'][0][0] == 'Anc4'
assert og.ogMap['Anc2'][0][0] == 'Anc4'
assert og.ogMap['Anc3'][0][0] == 'Anc4'
assert 'Anc4' not in og.ogMap
assert og.ogMap['Anc5'][0][0] in ['HUMAN', 'CHIMP', 'Anc6', 'Anc7']
assert og.ogMap['Anc6'][0][0] in ['Anc5', 'MOUSE', 'RAT']
assert og.ogMap['Anc7'][0][0] in ['Anc5', 'MOUSE', 'RAT']
og = GreedyOutgroup()
og.importTree(mcTree)
candidates = set(['HUMAN', 'CHIMP', 'RAT'])
candidateFrac = 1
og.greedy(candidateSet=candidates, candidateChildFrac=1.0)
assert og.ogMap['Anc1'][0][0] == 'Anc7'
assert og.ogMap['Anc2'][0][0] == 'Anc7'
assert og.ogMap['Anc3'][0][0] == 'Anc7'
assert 'Anc4' not in og.ogMap
assert og.ogMap['Anc5'][0][0] in ['HUMAN', 'CHIMP', 'Anc7']
assert og.ogMap['Anc6'][0][0] == 'RAT'
assert og.ogMap['Anc7'][0][0] == 'RAT'
def testMultipleOutgroupsOnRandomTrees(self):
for tree in self.mcTrees:
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(candidateChildFrac=0.5, maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
def testMultipleOutgroupsOnRandomTrees(self):
for tree in self.mcTrees:
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(candidateChildFrac=0.5, maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(
map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
def testJustLeaves(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set([self.borMcTree.getName(x) for x in self.borMcTree.getLeaves()])
og.greedy(candidateSet=candidates, candidateChildFrac=2.)
assert og.ogMap['Anc1'][0][0] == 'HUMAN'
assert og.ogMap['Anc2'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc3'][0][0] in ['PIG', 'COW']
assert og.ogMap['Anc4'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc5'][0][0] == 'HUMAN'
assert og.ogMap['Anc6'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc7'][0][0] == 'BABOON'
def testJustLeaves(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set(
[self.borMcTree.getName(x) for x in self.borMcTree.getLeaves()])
og.greedy(candidateSet=candidates, candidateChildFrac=2.)
assert og.ogMap['Anc1'][0][0] == 'HUMAN'
assert og.ogMap['Anc2'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc3'][0][0] in ['PIG', 'COW']
assert og.ogMap['Anc4'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc5'][0][0] == 'HUMAN'
assert og.ogMap['Anc6'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc7'][0][0] == 'BABOON'
def testGeneralConstrainedBetterThanLeaves(self):
for tree in self.mcTrees:
og1 = GreedyOutgroup()
og1.importTree(tree)
candidates = set([tree.getName(x) for x in tree.getLeaves()])
og1.greedy(candidateSet=candidates, candidateChildFrac=2.)
og2 = GreedyOutgroup()
og2.importTree(tree)
og2.greedy(candidateSet=None, threshold=2)
for i in og1.ogMap:
assert i in og2.ogMap
dist1 = og1.ogMap[i][0][1]
dist2 = og2.ogMap[i][0][1]
assert dist2 <= dist1
def testJustLeaves(self):
tree = '((((HUMAN:0.006969,CHIMP:0.009727)Anc7:0.025291,BABOON:0.044568)Anc6:0.11,(MOUSE:0.072818,RAT:0.081244)Anc5:0.260342)Anc4:0.023260,((DOG:0.07,CAT:0.07)Anc3:0.087381,(PIG:0.06,COW:0.06)Anc2:0.104728)Anc1:0.04)Anc0;'
mcTree = MultiCactusTree(NXNewick().parseString(tree, addImpliedRoots = False))
mcTree.computeSubtreeRoots()
og = GreedyOutgroup()
og.importTree(mcTree)
candidates = set([mcTree.getName(x) for x in mcTree.getLeaves()])
og.greedy(candidateSet=candidates, candidateChildFrac=2.)
assert og.ogMap['Anc1'][0][0] == 'HUMAN'
assert og.ogMap['Anc2'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc3'][0][0] in ['PIG', 'COW']
assert og.ogMap['Anc4'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc5'][0][0] == 'HUMAN'
assert og.ogMap['Anc6'][0][0] in ['CAT', 'DOG']
assert og.ogMap['Anc7'][0][0] == 'BABOON'
def testNoOutgroupIsADescendantOfAnother(self):
"""No two outgroups should be on the same path to the root."""
for tree in self.mcTrees:
tree.nameUnlabeledInternalNodes()
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(maxNumOutgroups=3)
for source in og.ogMap:
for (sink1, _) in og.ogMap[source]:
for (sink2, _) in og.ogMap[source]:
if sink1 != sink2:
sink1Id = tree.nameToId[sink1]
sink2Id = tree.nameToId[sink2]
assert sink1Id not in tree.postOrderTraversal(sink2Id)
assert sink2Id not in tree.postOrderTraversal(sink1Id)
def testGeneralConstrainedBetterThanLeaves(self):
for tree in self.mcTrees:
og1 = GreedyOutgroup()
og1.importTree(tree)
candidates = set([tree.getName(x) for x in tree.getLeaves()])
og1.greedy(candidateSet=candidates, candidateChildFrac=2.)
og2 = GreedyOutgroup()
og2.importTree(tree)
og2.greedy(candidateSet=None, threshold=2)
for i in og1.ogMap:
assert i in og2.ogMap
dist1 = og1.ogMap[i][0][1]
dist2 = og2.ogMap[i][0][1]
assert dist2 <= dist1
def testZeroThreshold(self):
"""A threshold of 0 should produce outgroup sets that cause no additional depth in the resulting schedule."""
tree = self.backboneTree
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(candidateSet=set(['Homo_sapiens', 'Mus_musculus']),threshold=0, maxNumOutgroups=3, candidateChildFrac=0.75)
og.greedy(threshold=0, maxNumOutgroups=3, candidateChildFrac=0.75)
htable = og.heightTable()
for node, outgroups in og.ogMap.items():
for outgroup, _ in outgroups:
# For the outgroup assignment to create no
# additional dependencies, each outgroup must have
# a height lower than the node it's outgroup to
# (or be a leaf)
self.assertTrue(htable[tree.getNodeId(outgroup)] < htable[tree.getNodeId(node)] \
or htable[tree.getNodeId(outgroup)] == 0)
def testMultipleOutgroupsJustLeaves(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set([self.borMcTree.getName(x) for x in self.borMcTree.getLeaves()])
og.greedy(candidateSet=candidates, candidateChildFrac=2.,
maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
# ordering is important!
assert map(itemgetter(0), og.ogMap['Anc1']) == ['HUMAN', 'CHIMP',
'BABOON']
assert og.ogMap['Anc7'][0][0] == 'BABOON'
assert og.ogMap['Anc7'][1][0] in ['CAT', 'DOG']
assert og.ogMap['Anc7'][2][0] in ['CAT', 'DOG']
def testMultipleOutgroups(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
og.greedy(candidateChildFrac=0.5, maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
# ordering is important!
assert map(itemgetter(0), og.ogMap['Anc4']) == ['Anc1']
assert map(itemgetter(0), og.ogMap['Anc7']) == ['BABOON', 'Anc1',
'Anc5']
# We avoid cycles, and choose post-order first, so this only
# uses leaves.
assert map(itemgetter(0), og.ogMap['Anc1']) == ['HUMAN', 'CHIMP',
'BABOON']
def testNoOutgroupIsADescendantOfAnother(self):
"""No two outgroups should be on the same path to the root."""
for tree in self.mcTrees:
tree.nameUnlabeledInternalNodes()
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(maxNumOutgroups=3)
for source in og.ogMap:
for (sink1, _) in og.ogMap[source]:
for (sink2, _) in og.ogMap[source]:
if sink1 != sink2:
sink1Id = tree.nameToId[sink1]
sink2Id = tree.nameToId[sink2]
assert sink1Id not in tree.postOrderTraversal(
sink2Id)
assert sink2Id not in tree.postOrderTraversal(
sink1Id)
def testMultipleOutgroups(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
og.greedy(candidateChildFrac=0.5, maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(
map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
# ordering is important!
assert map(itemgetter(0), og.ogMap['Anc4']) == ['Anc1']
assert map(itemgetter(0),
og.ogMap['Anc7']) == ['BABOON', 'Anc1', 'Anc5']
# We avoid cycles, and choose post-order first, so this only
# uses leaves.
assert map(itemgetter(0),
og.ogMap['Anc1']) == ['HUMAN', 'CHIMP', 'BABOON']
def testZeroThreshold(self):
"""A threshold of 0 should produce outgroup sets that cause no additional depth in the resulting schedule."""
tree = self.backboneTree
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(candidateSet=set(['Homo_sapiens', 'Mus_musculus']),
threshold=0,
maxNumOutgroups=3,
candidateChildFrac=0.75)
og.greedy(threshold=0, maxNumOutgroups=3, candidateChildFrac=0.75)
htable = og.heightTable()
for node, outgroups in og.ogMap.items():
for outgroup, _ in outgroups:
# For the outgroup assignment to create no
# additional dependencies, each outgroup must have
# a height lower than the node it's outgroup to
# (or be a leaf)
self.assertTrue(htable[tree.getNodeId(outgroup)] < htable[tree.getNodeId(node)] \
or htable[tree.getNodeId(outgroup)] == 0)
def testMultipleOutgroups(self):
tree = '((((HUMAN:0.006969,CHIMP:0.009727)Anc7:0.025291,BABOON:0.044568)Anc6:0.11,(MOUSE:0.072818,RAT:0.081244)Anc5:0.260342)Anc4:0.023260,((DOG:0.07,CAT:0.07)Anc3:0.087381,(PIG:0.06,COW:0.06)Anc2:0.104728)Anc1:0.04)Anc0;'
mcTree = MultiCactusTree(NXNewick().parseString(tree, addImpliedRoots = False))
mcTree.computeSubtreeRoots()
og = GreedyOutgroup()
og.importTree(mcTree)
og.greedy(candidateChildFrac=0.5, maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
# ordering is important!
assert map(itemgetter(0), og.ogMap['Anc4']) == ['Anc1']
assert map(itemgetter(0), og.ogMap['Anc7']) == ['BABOON', 'Anc1',
'Anc5']
# We avoid cycles, and choose post-order first, so this only
# uses leaves.
assert map(itemgetter(0), og.ogMap['Anc1']) == ['HUMAN', 'CHIMP',
'BABOON']
def testMultipleOutgroupsJustLeaves(self):
tree = '((((HUMAN:0.006969,CHIMP:0.009727)Anc7:0.025291,BABOON:0.044568)Anc6:0.11,(MOUSE:0.072818,RAT:0.081244)Anc5:0.260342)Anc4:0.023260,((DOG:0.07,CAT:0.07)Anc3:0.087381,(PIG:0.06,COW:0.06)Anc2:0.104728)Anc1:0.04)Anc0;'
mcTree = MultiCactusTree(NXNewick().parseString(tree, addImpliedRoots = False))
mcTree.computeSubtreeRoots()
og = GreedyOutgroup()
og.importTree(mcTree)
candidates = set([mcTree.getName(x) for x in mcTree.getLeaves()])
og.greedy(candidateSet=candidates, candidateChildFrac=2.,
maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
# ordering is important!
assert map(itemgetter(0), og.ogMap['Anc1']) == ['HUMAN', 'CHIMP',
'BABOON']
assert og.ogMap['Anc7'][0][0] == 'BABOON'
assert og.ogMap['Anc7'][1][0] in ['CAT', 'DOG']
assert og.ogMap['Anc7'][2][0] in ['CAT', 'DOG']
def testMultipleOutgroupsJustLeaves(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set(
[self.borMcTree.getName(x) for x in self.borMcTree.getLeaves()])
og.greedy(candidateSet=candidates,
candidateChildFrac=2.,
maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# and for all entries, the closest must be first.
assert all(
map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
# ordering is important!
assert map(itemgetter(0),
og.ogMap['Anc1']) == ['HUMAN', 'CHIMP', 'BABOON']
assert og.ogMap['Anc7'][0][0] == 'BABOON'
assert og.ogMap['Anc7'][1][0] in ['CAT', 'DOG']
assert og.ogMap['Anc7'][2][0] in ['CAT', 'DOG']
def testMultipleIdenticalRunsProduceSameResult(self):
"""The code now allows for multiple greedy() calls with different
candidate sets, so that some outgroups can be 'preferred' over
others without being the only candidates.
Check that running greedy() multiple times with the same
parameters gives the same result as running it once.
"""
for tree in self.mcTrees:
ogOnce = GreedyOutgroup()
ogOnce.importTree(tree)
ogOnce.greedy(maxNumOutgroups=3)
ogMultipleTimes = GreedyOutgroup()
ogMultipleTimes.importTree(tree)
ogMultipleTimes.greedy(maxNumOutgroups=3)
ogMultipleTimes.greedy(maxNumOutgroups=3)
ogMultipleTimes.greedy(maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, ogMultipleTimes.ogMap.values()))
# and for all entries, the closest must be first.
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
ogMultipleTimes.ogMap.values()))
# Check that the maps are equal. Can't compare them
# directly since python will convert them to ordered
# association lists.
assert len(ogOnce.ogMap) == len(ogMultipleTimes.ogMap)
for i in ogOnce.ogMap:
assert i in ogMultipleTimes.ogMap
assert ogOnce.ogMap[i] == ogMultipleTimes.ogMap[i]
def testPreferredCandidateSets(self):
"""Test that running greedy() multiple times with different candidate
sets will behave properly, i.e. keep all the existing outgroup
assignments and fill in more on the second run."""
for tree in self.mcTrees:
ogOnce = GreedyOutgroup()
ogOnce.importTree(tree)
nodes = [j for j in tree.postOrderTraversal()]
candidateSet = set([
tree.getName(i)
for i in random.sample(nodes, min(20, len(nodes)))
])
ogOnce.greedy(candidateSet=candidateSet, maxNumOutgroups=3)
ogTwice = GreedyOutgroup()
ogTwice.importTree(tree)
ogTwice.greedy(candidateSet=candidateSet, maxNumOutgroups=3)
ogTwice.greedy(maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, ogTwice.ogMap.values()))
# and for all entries, the closest must be first.
assert all(
map(lambda x: x == sorted(x, key=itemgetter(1)),
ogTwice.ogMap.values()))
for node in ogTwice.ogMap:
if node in ogOnce.ogMap:
# the ogMap entry in ogOnce should be a subset of the ogMap entry for ogTwice
oneRunOutgroups = ogOnce.ogMap[node]
twoRunOutgroups = ogTwice.ogMap[node]
assert len(twoRunOutgroups) >= len(oneRunOutgroups)
for i in oneRunOutgroups:
assert i in twoRunOutgroups
def testMultipleIdenticalRunsProduceSameResult(self):
"""The code now allows for multiple greedy() calls with different
candidate sets, so that some outgroups can be 'preferred' over
others without being the only candidates.
Check that running greedy() multiple times with the same
parameters gives the same result as running it once.
"""
for tree in self.mcTrees:
ogOnce = GreedyOutgroup()
ogOnce.importTree(tree)
ogOnce.greedy(maxNumOutgroups=3)
ogMultipleTimes = GreedyOutgroup()
ogMultipleTimes.importTree(tree)
ogMultipleTimes.greedy(maxNumOutgroups=3)
ogMultipleTimes.greedy(maxNumOutgroups=3)
ogMultipleTimes.greedy(maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(
map(lambda x: len(x) <= 3, ogMultipleTimes.ogMap.values()))
# and for all entries, the closest must be first.
assert all(
map(lambda x: x == sorted(x, key=itemgetter(1)),
ogMultipleTimes.ogMap.values()))
# Check that the maps are equal. Can't compare them
# directly since python will convert them to ordered
# association lists.
assert len(ogOnce.ogMap) == len(ogMultipleTimes.ogMap)
for i in ogOnce.ogMap:
assert i in ogMultipleTimes.ogMap
assert ogOnce.ogMap[i] == ogMultipleTimes.ogMap[i]
def testPreferredCandidateSets(self):
"""Test that running greedy() multiple times with different candidate
sets will behave properly, i.e. keep all the existing outgroup
assignments and fill in more on the second run."""
for tree in self.mcTrees:
ogOnce = GreedyOutgroup()
ogOnce.importTree(tree)
nodes = [j for j in tree.postOrderTraversal()]
candidateSet = set([tree.getName(i) for i in random.sample(nodes, min(20, len(nodes)))])
ogOnce.greedy(candidateSet=candidateSet, maxNumOutgroups=3)
ogTwice = GreedyOutgroup()
ogTwice.importTree(tree)
ogTwice.greedy(candidateSet=candidateSet, maxNumOutgroups=3)
ogTwice.greedy(maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, ogTwice.ogMap.values()))
# and for all entries, the closest must be first.
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
ogTwice.ogMap.values()))
for node in ogTwice.ogMap:
if node in ogOnce.ogMap:
# the ogMap entry in ogOnce should be a subset of the ogMap entry for ogTwice
oneRunOutgroups = ogOnce.ogMap[node]
twoRunOutgroups = ogTwice.ogMap[node]
assert len(twoRunOutgroups) >= len(oneRunOutgroups)
for i in oneRunOutgroups:
assert i in twoRunOutgroups
def testCandidates(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set(['HUMAN', 'CHIMP', 'RAT'])
og.greedy(candidateSet=candidates, candidateChildFrac=0.5)
assert og.ogMap['Anc1'][0][0] == 'Anc4'
assert og.ogMap['Anc2'][0][0] == 'Anc4'
assert og.ogMap['Anc3'][0][0] == 'Anc4'
assert 'Anc4' not in og.ogMap
assert og.ogMap['Anc5'][0][0] in ['HUMAN', 'CHIMP', 'Anc6', 'Anc7']
assert og.ogMap['Anc6'][0][0] in ['Anc5', 'MOUSE', 'RAT']
assert og.ogMap['Anc7'][0][0] in ['Anc5', 'MOUSE', 'RAT']
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set(['HUMAN', 'CHIMP', 'RAT'])
og.greedy(candidateSet=candidates, candidateChildFrac=1.0)
assert og.ogMap['Anc1'][0][0] == 'Anc7'
assert og.ogMap['Anc2'][0][0] == 'Anc7'
assert og.ogMap['Anc3'][0][0] == 'Anc7'
assert 'Anc4' not in og.ogMap
assert og.ogMap['Anc5'][0][0] in ['HUMAN', 'CHIMP', 'Anc7']
assert og.ogMap['Anc6'][0][0] == 'RAT'
assert og.ogMap['Anc7'][0][0] == 'RAT'
def testCandidates(self):
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set(['HUMAN', 'CHIMP', 'RAT'])
og.greedy(candidateSet=candidates, candidateChildFrac=0.5)
assert og.ogMap['Anc1'][0][0] == 'Anc4'
assert og.ogMap['Anc2'][0][0] == 'Anc4'
assert og.ogMap['Anc3'][0][0] == 'Anc4'
assert 'Anc4' not in og.ogMap
assert og.ogMap['Anc5'][0][0] in ['HUMAN', 'CHIMP', 'Anc6', 'Anc7']
assert og.ogMap['Anc6'][0][0] in ['Anc5', 'MOUSE', 'RAT']
assert og.ogMap['Anc7'][0][0] in ['Anc5', 'MOUSE', 'RAT']
og = GreedyOutgroup()
og.importTree(self.borMcTree)
candidates = set(['HUMAN', 'CHIMP', 'RAT'])
og.greedy(candidateSet=candidates, candidateChildFrac=1.0)
assert og.ogMap['Anc1'][0][0] == 'Anc7'
assert og.ogMap['Anc2'][0][0] == 'Anc7'
assert og.ogMap['Anc3'][0][0] == 'Anc7'
assert 'Anc4' not in og.ogMap
assert og.ogMap['Anc5'][0][0] in ['HUMAN', 'CHIMP', 'Anc7']
assert og.ogMap['Anc6'][0][0] == 'RAT'
assert og.ogMap['Anc7'][0][0] == 'RAT'
