def setup (self):
"""
Build a tree that starts from root, radiates to ABC and DE and thence to AB (and
A & B) and D and E.
Our tree is:
- root
- ABC
- AB
- A
- B
- C
- DE
- D
- E
"""
t = Tree()
r = t.add_root ({'title': 'root'})
node_abc, b = t.add_node (r, {'title': 'ABC'})
node_de, b = t.add_node (r, {'title': 'DE'})
node_ab, b = t.add_node (node_abc, {'title': 'AB'})
node_c, b = t.add_node (node_abc, {'title': 'C'})
node_a, b = t.add_node (node_ab, {'title': 'A'})
node_b, b = t.add_node (node_ab, {'title': 'B'})
node_d, b = t.add_node (node_de, {'title': 'D'})
node_e, b = t.add_node (node_de, {'title': 'E'})
# record for use in test functions
self.tree = t
self.nodes = {}
for n in [r, node_a, node_b, node_c, node_d, node_e, node_ab, node_abc, node_de]:
self.nodes[n.title] = n
def test():
"""
Some code to walk the script through its paces.
"""
# make a tree
from phylo.core.tree import Tree
t = Tree()
r = t.add_root ({'title': 'root'})
nabcd, b = t.add_node (r, {'title': 'ABCD'})
nef, b = t.add_node (r, {'title': 'EF'})
nab, b = t.add_node (nabcd, {'title': 'AB'})
ncd, b = t.add_node (nabcd, {'title': 'CD'})
na, b = t.add_node (nab, {'title': 'A'})
nb, b = t.add_node (nab, {'title': 'B'})
nc, b = t.add_node (ncd, {'title': 'C'})
nd, b = t.add_node (ncd, {'title': 'D'})
ne, b = t.add_node (nef, {'title': 'E'})
nf, b = t.add_node (nef, {'title': 'F'})
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio.Align import MultipleSeqAlignment
seqdata = [
['A', 'XYGT'],
['B', 'AYGT'],
['C', 'ACGT'],
['D', 'ACGT'],
['E', 'ACGT'],
['F', 'ACGT'],
]
srs = [SeqRecord (Seq (x[1]), id=x[0], name=x[0]) for x in seqdata]
aln = MultipleSeqAlignment (srs)
return t, aln
def setup(self):
# create a test tree
t = Tree()
a = t.add_root({'title': 'A'})
b, br = t.add_node(a, {'title': 'B'})
c, br = t.add_node(a, {'title': 'C'})
d, br = t.add_node(b, {'title': 'D'})
e, br = t.add_node(b, {'title': 'E'})
f, br = t.add_node(c, {'title': 'F'})
g, br = t.add_node(c, {'title': 'G'})
self.tree = t
def setup(self):
# create a test tree
t = Tree()
a = t.add_root ({'title': 'A'})
b, br = t.add_node (a, {'title': 'B'})
c, br = t.add_node (a, {'title': 'C'})
d, br = t.add_node (b, {'title': 'D'})
e, br = t.add_node (b, {'title': 'E'})
f, br = t.add_node (c, {'title': 'F'})
g, br = t.add_node (c, {'title': 'G'})
self.tree = t
def setup(self):
"""
Build a tree that starts from root, radiates to AB, CD. EF and then
A to F.
"""
t = Tree()
r = t.add_root({'title': 'root'})
nab, b = t.add_node(r, {'title': 'AB'},
branch_props={
'title': 'root-AB',
'distance': 1.0
})
na, b = t.add_node(nab, {'title': 'A'},
branch_props={
'title': 'A-AB',
'distance': 1.1
})
nb, b = t.add_node(nab, {'title': 'B'},
branch_props={
'title': 'B-AB',
'distance': 1.2
})
ncd, b = t.add_node(r, {'title': 'CD'},
branch_props={
'title': 'root-CD',
'distance': 1.3
})
nc, b = t.add_node(ncd, {'title': 'C'},
branch_props={
'title': 'C-CD',
'distance': 1.4
})
nd, b = t.add_node(ncd, {'title': 'D'},
branch_props={
'title': 'D-CD',
'distance': 1.5
})
nef, b = t.add_node(r, {'title': 'EF'},
branch_props={
'title': 'root-EF',
'distance': 1.6
})
ne, b = t.add_node(nef, {'title': 'E'},
branch_props={
'title': 'E-EF',
'distance': 1.7
})
nf, b = t.add_node(nef, {'title': 'F'},
branch_props={
'title': 'F-EF',
'distance': 1.8
})
self.tree = t
def setup(self):
# make up a dummy tree to test upon
from phylo.core.tree import Tree
t = Tree()
a = t.add_root ({'title': 'A'})
b, br = t.add_node (a, {'title': 'B'})
c, br = t.add_node (a, {'title': 'C'})
d, br = t.add_node (b, {'title': 'D'})
e, br = t.add_node (b, {'title': 'E'})
f, br = t.add_node (c, {'title': 'F'})
g, br = t.add_node (c, {'title': 'G'})
self.tree = t
# record the nodes for later convenience
self.nodes = dict ([(n.title, n) for n in t.nodes])
def setup(self):
# make up a dummy tree to test upon
from phylo.core.tree import Tree
t = Tree()
a = t.add_root({'title': 'A'})
b, br = t.add_node(a, {'title': 'B'})
c, br = t.add_node(a, {'title': 'C'})
d, br = t.add_node(b, {'title': 'D'})
e, br = t.add_node(b, {'title': 'E'})
f, br = t.add_node(c, {'title': 'F'})
g, br = t.add_node(c, {'title': 'G'})
self.tree = t
# record the nodes for later convenience
self.nodes = dict([(n.title, n) for n in t.nodes])
def setup (self):
"""
Build a tree that starts from root, radiates to AB, CD. EF and then
A to F.
"""
t = Tree()
r = t.add_root ({'title': 'root'})
nab, b = t.add_node (r, {'title': 'AB'}, branch_props={'title': 'root-AB', 'distance': 1.0})
na, b = t.add_node (nab, {'title': 'A'}, branch_props={'title': 'A-AB', 'distance': 1.1})
nb, b = t.add_node (nab, {'title': 'B'}, branch_props={'title': 'B-AB', 'distance': 1.2})
ncd, b = t.add_node (r, {'title': 'CD'}, branch_props={'title': 'root-CD', 'distance': 1.3})
nc, b = t.add_node (ncd, {'title': 'C'}, branch_props={'title': 'C-CD', 'distance': 1.4})
nd, b = t.add_node (ncd, {'title': 'D'}, branch_props={'title': 'D-CD', 'distance': 1.5})
nef, b = t.add_node (r, {'title': 'EF'}, branch_props={'title': 'root-EF', 'distance': 1.6})
ne, b = t.add_node (nef, {'title': 'E'}, branch_props={'title': 'E-EF', 'distance': 1.7})
nf, b = t.add_node (nef, {'title': 'F'}, branch_props={'title': 'F-EF', 'distance': 1.8})
self.tree = t
def setup(self):
"""
Build a tree that starts from root, radiates to AB, CD. EF and then
A to F.
Our tree is:
- root
- ABC
- AB
- A
- B
- C
- DE
- D
- E
"""
t = Tree()
r = t.add_root({'title': 'root'})
node_abc, b = t.add_node(r, {'title': 'ABC'})
node_de, b = t.add_node(r, {'title': 'DE'})
node_ab, b = t.add_node(node_abc, {'title': 'AB'})
node_c, b = t.add_node(node_abc, {'title': 'C'})
node_a, b = t.add_node(node_ab, {'title': 'A'})
node_b, b = t.add_node(node_ab, {'title': 'B'})
node_d, b = t.add_node(node_de, {'title': 'D'})
node_e, b = t.add_node(node_de, {'title': 'E'})
# record for use in test functions
self.tree = t
self.nodes = {}
for n in [
r, node_a, node_b, node_c, node_d, node_e, node_ab, node_abc,
node_de
]:
self.nodes[n.title] = n
self.solo_tree = Tree()
self.solo_tree.add_root()
# create a test tree
from phylo.core.tree import Tree
t = Tree()
a = t.add_root ({'title': 'A'})
b, br = t.add_node (a, {'title': 'B'})
c, br = t.add_node (a, {'title': 'C'})
d, br = t.add_node (b, {'title': 'D'})
e, br = t.add_node (b, {'title': 'E'})
f, br = t.add_node (c, {'title': 'F'})
g, br = t.add_node (c, {'title': 'G'})
for n in t.nodes:
print n
print t.node_children (n)
print
# create a test tree
from phylo.core.tree import Tree
t = Tree()
a = t.add_root({'title': 'A'})
b, br = t.add_node(a, {'title': 'B'})
c, br = t.add_node(a, {'title': 'C'})
d, br = t.add_node(b, {'title': 'D'})
e, br = t.add_node(b, {'title': 'E'})
f, br = t.add_node(c, {'title': 'F'})
g, br = t.add_node(c, {'title': 'G'})
for n in t.nodes:
print n
print t.node_children(n)
print
class TestNodeAccessors(object):
def setup(self):
"""
Build a tree that starts from root, radiates to AB, CD. EF and then
A to F.
Our tree is:
- root
- ABC
- AB
- A
- B
- C
- DE
- D
- E
"""
t = Tree()
r = t.add_root({'title': 'root'})
node_abc, b = t.add_node(r, {'title': 'ABC'})
node_de, b = t.add_node(r, {'title': 'DE'})
node_ab, b = t.add_node(node_abc, {'title': 'AB'})
node_c, b = t.add_node(node_abc, {'title': 'C'})
node_a, b = t.add_node(node_ab, {'title': 'A'})
node_b, b = t.add_node(node_ab, {'title': 'B'})
node_d, b = t.add_node(node_de, {'title': 'D'})
node_e, b = t.add_node(node_de, {'title': 'E'})
# record for use in test functions
self.tree = t
self.nodes = {}
for n in [
r, node_a, node_b, node_c, node_d, node_e, node_ab, node_abc,
node_de
]:
self.nodes[n.title] = n
self.solo_tree = Tree()
self.solo_tree.add_root()
def teardown(self):
pass
def test_neighbours(self):
neighbours = [
['ABC', ['root', 'AB', 'C']],
['AB', ['ABC', 'A', 'B']],
['A', ['AB']],
['B', ['AB']],
['DE', ['root', 'D', 'E']],
['D', ['DE']],
['E', ['DE']],
['root', ['ABC', 'DE']],
]
for r in neighbours:
n = self.nodes[r[0]]
names = [ne.title for ne in self.tree.node_neighbours(n)]
assert are_lists_equal(names,
r[1]), "'%s' is not '%s'" % (names, r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
print self.solo_tree.node_neighbours(solo_node)
assert (self.solo_tree.node_neighbours(solo_node) == [])
def test_children(self):
children = [
['ABC', ['AB', 'C']],
['AB', ['A', 'B']],
['A', []],
['B', []],
['DE', ['D', 'E']],
['D', []],
['E', []],
['root', ['ABC', 'DE']],
]
for r in children:
print "Testing %s ..." % r
n = self.nodes[r[0]]
print "Node is %s ..." % n
names = [ne.title for ne in self.tree.node_children(n)]
assert are_lists_equal(names,
r[1]), "'%s' is not '%s'" % (names, r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.node_children(solo_node) == [])
def test_parents(self):
parents = [
['ABC', 'root'],
['AB', 'ABC'],
['A', 'AB'],
['B', 'AB'],
['DE', 'root'],
['D', 'DE'],
['E', 'DE'],
['root', None],
]
for r in parents:
n = self.nodes[r[0]]
node = self.tree.node_parent(n)
if node:
node = node.title
assert (node == r[1]), "'%s' is not '%s'" % (node, r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.node_parent(solo_node) == None)
def test_is_tip(self):
nodes = [
['ABC', False],
['AB', False],
['A', True],
['B', True],
['DE', False],
['D', True],
['E', True],
['root', False],
]
for r in nodes:
assert (self.tree.is_node_tip(self.nodes[r[0]]) == r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.is_node_tip(solo_node))
def test_is_internal(self):
nodes = [
['ABC', True],
['AB', True],
['A', False],
['B', False],
['DE', True],
['D', False],
['E', False],
['root', True],
]
for r in nodes:
assert (self.tree.is_node_internal(self.nodes[r[0]]) == r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.is_node_internal(solo_node) == False)
def test_is_root(self):
nodes = [
['ABC', False],
['AB', False],
['A', False],
['B', False],
['DE', False],
['D', False],
['E', False],
['root', True],
]
for r in nodes:
assert (self.tree.is_node_root(self.nodes[r[0]]) == r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.is_node_root(solo_node))
### END ####################################################################
class TestNodeAccessors (object):
def setup (self):
"""
Build a tree that starts from root, radiates to AB, CD. EF and then
A to F.
Our tree is:
- root
- ABC
- AB
- A
- B
- C
- DE
- D
- E
"""
t = Tree()
r = t.add_root ({'title': 'root'})
node_abc, b = t.add_node (r, {'title': 'ABC'})
node_de, b = t.add_node (r, {'title': 'DE'})
node_ab, b = t.add_node (node_abc, {'title': 'AB'})
node_c, b = t.add_node (node_abc, {'title': 'C'})
node_a, b = t.add_node (node_ab, {'title': 'A'})
node_b, b = t.add_node (node_ab, {'title': 'B'})
node_d, b = t.add_node (node_de, {'title': 'D'})
node_e, b = t.add_node (node_de, {'title': 'E'})
# record for use in test functions
self.tree = t
self.nodes = {}
for n in [r, node_a, node_b, node_c, node_d, node_e, node_ab, node_abc, node_de]:
self.nodes[n.title] = n
self.solo_tree = Tree()
self.solo_tree.add_root()
def teardown (self):
pass
def test_neighbours (self):
neighbours = [
['ABC', ['root', 'AB', 'C']],
['AB', ['ABC', 'A', 'B']],
['A', ['AB']],
['B', ['AB']],
['DE', ['root', 'D', 'E']],
['D', ['DE']],
['E', ['DE']],
['root', ['ABC', 'DE']],
]
for r in neighbours:
n = self.nodes[r[0]]
names = [ne.title for ne in self.tree.node_neighbours (n)]
assert are_lists_equal (names, r[1]), "'%s' is not '%s'" % (names, r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
print self.solo_tree.node_neighbours(solo_node)
assert (self.solo_tree.node_neighbours(solo_node) == [])
def test_children (self):
children = [
['ABC', ['AB', 'C']],
['AB', ['A', 'B']],
['A', []],
['B', []],
['DE', ['D', 'E']],
['D', []],
['E', []],
['root', ['ABC', 'DE']],
]
for r in children:
print "Testing %s ..." % r
n = self.nodes[r[0]]
print "Node is %s ..." % n
names = [ne.title for ne in self.tree.node_children (n)]
assert are_lists_equal (names, r[1]), "'%s' is not '%s'" % (names, r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.node_children(solo_node) == [])
def test_parents (self):
parents = [
['ABC', 'root'],
['AB', 'ABC'],
['A', 'AB'],
['B', 'AB'],
['DE', 'root'],
['D', 'DE'],
['E', 'DE'],
['root', None],
]
for r in parents:
n = self.nodes[r[0]]
node = self.tree.node_parent (n)
if node:
node = node.title
assert (node == r[1]), "'%s' is not '%s'" % (node, r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.node_parent(solo_node) == None)
def test_is_tip (self):
nodes = [
['ABC', False],
['AB', False],
['A', True],
['B', True],
['DE', False],
['D', True],
['E', True],
['root', False],
]
for r in nodes:
assert (self.tree.is_node_tip (self.nodes[r[0]]) == r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.is_node_tip(solo_node))
def test_is_internal (self):
nodes = [
['ABC', True],
['AB', True],
['A', False],
['B', False],
['DE', True],
['D', False],
['E', False],
['root', True],
]
for r in nodes:
assert (self.tree.is_node_internal (self.nodes[r[0]]) == r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.is_node_internal(solo_node) == False)
def test_is_root (self):
nodes = [
['ABC', False],
['AB', False],
['A', False],
['B', False],
['DE', False],
['D', False],
['E', False],
['root', True],
]
for r in nodes:
assert (self.tree.is_node_root (self.nodes[r[0]]) == r[1])
# test the odd case of a tree with a single node
solo_node = self.solo_tree.nodes[0]
assert (self.solo_tree.is_node_root(solo_node))
### END ####################################################################