def testDynamicOutgroupsJustLeaves(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 = DynamicOutgroup()
og.importTree(mcTree, self.blanchetteSeqMap)
og.compute(maxNumOutgroups=3, sequenceLossWeight=0.)
# 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 og.ogMap['Anc1'][0][0] == 'HUMAN'
assert og.ogMap['Anc7'][0][0] == 'BABOON'
og = DynamicOutgroup()
og.importTree(mcTree, self.blanchetteSeqMap)
og.compute(maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# we keep dynamic outgroups sorted by distance too
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
def testDynamicOutgroupsOnRandomTrees(self):
for tree, seqMap in zip(self.mcTrees, self.dummySeqMaps):
degree = max([len(tree.getChildren(x)) for x in
tree.breadthFirstTraversal()])
if degree < 8:
og = DynamicOutgroup()
og.edgeLen = 5
og.importTree(tree, seqMap)
og.compute(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.
# (this will be true because all sequences are the same)
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
def testDynamicOutgroupsOnRandomTrees(self):
for tree, seqMap in zip(self.mcTrees, self.dummySeqMaps):
degree = max([
len(tree.getChildren(x)) for x in tree.breadthFirstTraversal()
])
if degree < 8:
og = DynamicOutgroup()
og.edgeLen = 5
og.importTree(tree, seqMap)
og.compute(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.
# (this will be true because all sequences are the same)
assert all(
map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
def testDynamicOutgroupsJustLeaves(self):
og = DynamicOutgroup()
og.importTree(self.borMcTree, self.blanchetteSeqMap)
og.compute(maxNumOutgroups=3, sequenceLossWeight=0.)
# 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 og.ogMap['Anc1'][0][0] == 'HUMAN'
assert og.ogMap['Anc7'][0][0] == 'BABOON'
og = DynamicOutgroup()
og.importTree(self.borMcTree, self.blanchetteSeqMap)
og.compute(maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# we keep dynamic outgroups sorted by distance too
assert all(map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))
def testDynamicOutgroupsJustLeaves(self):
og = DynamicOutgroup()
og.importTree(self.borMcTree, self.blanchetteSeqMap)
og.compute(maxNumOutgroups=3, sequenceLossWeight=0.)
# 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 og.ogMap['Anc1'][0][0] == 'HUMAN'
assert og.ogMap['Anc7'][0][0] == 'BABOON'
og = DynamicOutgroup()
og.importTree(self.borMcTree, self.blanchetteSeqMap)
og.compute(maxNumOutgroups=3)
# make sure all entries have <= 3 outgroups.
assert all(map(lambda x: len(x) <= 3, og.ogMap.values()))
# we keep dynamic outgroups sorted by distance too
assert all(
map(lambda x: x == sorted(x, key=itemgetter(1)),
og.ogMap.values()))