def testClusterNamingWithBootstraps(self):
tree = TreeNode.read(
StringIO(
"((F:20, ((A:11, B:12):10, (H:8, D:9):3):20)'0.7:G':30)root;"))
clusters = Tree2Tax().named_clusters(tree, 40)
self.assertSameClusters([['F'], _('A B D H')], clusters)
assert_equals(_('G.2 G.1'), [c.name() for c in clusters])
def testSimpleTwice(self):
tree = TreeNode.read(StringIO('((A:0.11, B:0.12)C:0.1, D:0.2)root;'))
clusters = Tree2Tax().named_clusters_for_several_thresholds(
tree, [0.25, 0.25])
self.assertSameClusterSets(
[[0.25, [['A', 'B'], ['D']]], [0.25, [['A', 'B'], ['D']]]],
clusters)
def testClusterNamingConventionsWithSomeUnnamed(self):
tree = TreeNode.read(
StringIO('((((A:11, B:12):10, D:9):20, F:20)G:30)root;'))
clusters = Tree2Tax().named_clusters(
tree, 0.05) #i.e. everything is a separate cluster
self.assertSameClusters([['A'], ['B'], ['D'], ['F']], clusters)
assert_equals(['G.1', 'G.2', 'G.3', 'G.4'],
[c.name() for c in clusters])
def testOppositeSorting(self):
tree = TreeNode.read(StringIO('((A:0.11, B:0.12)C:0.1, D:0.2)root;'))
clusters = Tree2Tax().named_clusters_for_several_thresholds(
tree, [0.05, 0.25])
self.assertSameClusterSets(
[[0.05, [['A'], ['B'], ['D']]], [0.25, [['A', 'B'], ['D']]]],
clusters)
assert_equals(_('C.1 C.2 Root'),
[c.name() for c in clusters[0].clusters])
def testNaming(self):
tree = TreeNode.read(
StringIO('((F:20, ((A:11, B:12):10, (H:8, D:9):3):20)G:30)root;'))
clusters = Tree2Tax().named_clusters_for_several_thresholds(
tree, [40, 25])
self.assertSameClusterSets(
[[25, [['F'], _('A B'), _('D H')]],
[40, [['F'], _('A B D H')]]], clusters)
assert_equals(_('G.3 G.1 G.2'),
[c.name() for c in clusters[0].clusters])
assert_equals(_('G.2 G.1'), [c.name() for c in clusters[1].clusters])
def testNamingWithBootstraps(self):
tree = TreeNode.read(
StringIO('((A:0.11, B:0.12)0.091:0.1, D:0.2)root;'))
clusters = Tree2Tax().named_clusters(tree, 0.05)
self.assertSameClusters([['A'], ['B'], ['D']], clusters)
assert_equals(_('Root.1 Root.2 Root.3'), [c.name() for c in clusters])
def testClusterNamingOnTwoInternalNodesReverseOrder(self):
tree = TreeNode.read(
StringIO('((F:20, ((A:11, B:12):10, (H:8, D:9):3):20)G:30)root;'))
clusters = Tree2Tax().named_clusters(tree, 40)
self.assertSameClusters([['F'], _('A B D H')], clusters)
assert_equals(_('G.2 G.1'), [c.name() for c in clusters])
def testClusterIntoThree(self):
tree = TreeNode.read(
StringIO(
'((((A:11, B:12)C:10, (H:8, D:9)I:3)E:20, F:20)G:30)root;'))
clusters = Tree2Tax().named_clusters(tree, 25)
self.assertSameClusters([_('A B'), _('D H'), ['F']], clusters)
def testClusterOnTwoInternalNodes(self):
tree = TreeNode.read(
StringIO(
'((((A:11, B:12)C:10, (H:8, D:9)I:3)E:20, F:20)G:30)root;'))
clusters = Tree2Tax().named_clusters(tree, 40)
self.assertSameClusters([_('A B D H'), ['F']], clusters)
def testClusterEverything(self):
tree = TreeNode.read(StringIO('((A:0.11, B:0.12)C:0.1, D:0.2)root;'))
clusters = Tree2Tax().named_clusters(tree, 0.5)
self.assertSameClusters([['A', 'B', 'D']], clusters)
assert_equals('Root', clusters[0].name())
def testNoClusering(self):
tree = TreeNode.read(StringIO('((A:0.11, B:0.12)C:0.1, D:0.2)root;'))
clusters = Tree2Tax().named_clusters(tree, 0.05)
self.assertSameClusters([['A'], ['B'], ['D']], clusters)
assert_equals(_('C.1 C.2 Root'), [c.name() for c in clusters])
def testSimple(self):
tree = TreeNode.read(StringIO('((A:0.11, B:0.12)C:0.1, D:0.2)root;'))
clusters = Tree2Tax().named_clusters(tree, 0.25)
self.assertSameClusters([['A', 'B'], ['D']], clusters)