def test():
import newick, ascii
n = newick.parse("(((a:1,b:2):3,(c:3,d:1):1,(e:0.5,f:3):2.5):1,g:4);")
v = ltt(n)
print ascii.render(n, scaled=1)
for t, n in v:
print t, n
def test():
import newick, ascii
n = newick.parse("(((a:1,b:2):3,(c:3,d:1):1,(e:0.5,f:3):2.5):1,g:4);")
v = ltt(n)
print(ascii.render(n, scaled=1))
for t, n in v:
print(t, n)
def default_from_tree(self, i, nareas):
t = newick.parse(self.model.treelist.trees[i].newick)
self.taxa = [n.label for n in t.leaves()]
self.labels = string.uppercase[:nareas]
self.nlabels = len(self.labels)
self.data = dict([(x, [False] * nareas) for x in self.taxa])
self.data = dict([(x, []) for x in self.taxa])
self.model.adjacencymatrix.default()
self.model.dm.default()
def __init__(self, newickstr, periods=None, root_age=None):
"""
newickstr: newick tree with branch lengths
periods: list of durations ordered from present to past
root_age: age of root node for branch length scaling
"""
self.root = newick.parse(newickstr)
phylo.polarize(self.root)
self.periods = periods
# initialize nodes (label interiors, etc)
# and collect leaves and postorder sequence
self.postorder_nodes = []
self.leaves = []
for i, node in enumerate(self.root.descendants(phylo.POSTORDER)):
node.tree = self
node.number = i
node.segments = []
if (not node.istip) and (not node.label):
node.label = str(node.number)
node.age = None
if node.istip:
#node.age = 0.0
self.leaves.append(node)
self.postorder_nodes.append(node)
self.root_age = root_age
if root_age:
self.calibrate(root_age)
self.label2node = dict([(n.label, n) for n in self.postorder_nodes ])
self.assign_node_ages()
## for node in self.postorder_nodes:
## if node.parent and (node.parent.age is None):
## node.parent.age = node.age + node.length
# initialize branch segments
for node in self.postorder_nodes:
if node.parent:
periods = self.periods
anc = node.parent.age
des = node.age
assert anc > des, "%s = %g, %s = %g\n%s" \
% (node.parent.label, anc, node.label, des,
self.root.render_ascii(scaled=1, minwidth=80))
t = des
for i, p in enumerate(periods):
s = sum(periods[:i+1])
if t < s:
duration = min((s - t, anc - t))
if duration > 0:
seg = BranchSegment(duration, i)
node.segments.append(seg)
t += p
if t > anc:
break
def errors(self):
try:
s = self.trees[0].newick
except:
return "no tree specified"
n = newick.parse(s)
leaves = [lf.label for lf in n.leaves()]
for x in self.model.datamatrix.data.keys():
if x not in leaves:
return "%s not found among tree tips" % x
def errors(self):
try:
s = self.trees[0].newick
except:
return "no tree specified"
n = newick.parse(s)
leaves = [ lf.label for lf in n.leaves() ]
for x in self.model.datamatrix.data.keys():
if x not in leaves:
return "%s not found among tree tips" % x
def default_from_tree(self, i, nareas):
t = newick.parse(self.model.treelist.trees[i].newick)
self.taxa = [ n.label for n in t.leaves() ]
self.labels = string.uppercase[:nareas]
self.nlabels = len(self.labels)
self.data = dict(
[ (x, [False]*nareas) for x in self.taxa ]
)
self.data = dict([ (x, []) for x in self.taxa ])
self.model.adjacencymatrix.default()
self.model.dm.default()
def test():
import newick
node = newick.parse("(a:3,(b:2,(c:4,d:5):1,(e:3,(f:1,g:1):2):2):2);")
for i, n in enumerate(node.iternodes()):
if not n.isleaf:
n.label = "node%s" % i
node.label = "root"
n2c = calc_node_positions(node, radius=100, scaled=False)
from matplotlib.patches import Arc, PathPatch
from matplotlib.collections import PatchCollection, LineCollection
import matplotlib.pyplot as P
f = P.figure()
a = f.add_subplot(111)
arcs = []
lines = []
for n in node.iternodes():
c = n2c[n]
if n.parent and n.children:
theta1 = n2c[n.children[0]].angle
theta2 = n2c[n.children[-1]].angle
arc = Arc((0, 0),
c.depth * 2,
c.depth * 2,
theta1=theta1,
theta2=theta2)
arcs.append(arc)
if n.parent:
p = n2c[n.parent]
px = math.cos(math.radians(c.angle)) * p.depth
py = math.sin(math.radians(c.angle)) * p.depth
lines.append(((c.x, c.y), (px, py)))
if n.label:
txt = a.annotate(n.label,
xy=(c.x, c.y),
xytext=(0, 0),
textcoords="offset points")
arcs = PatchCollection(arcs, match_original=True)
a.add_collection(arcs)
lines = LineCollection(lines)
a.add_collection(lines)
a.set_xlim((-100, 100))
a.set_ylim((-100, 100))
f.show()
def readmany(data, format="newick"):
"""Iterate over trees from a source."""
if type(data) in types.StringTypes:
if os.path.isfile(data):
data = open(data)
else:
data = StringIO(data)
if format == "newick":
for line in data:
yield newick.parse(line)
elif format == "nexus":
for rec in newick.nexus_iter(data):
yield rec.parse()
else:
raise Exception, "format '%s' not recognized" % format
data.close()
def test():
import newick
node = newick.parse("(a:3,(b:2,(c:4,d:5):1,(e:3,(f:1,g:1):2):2):2);")
for i, n in enumerate(node.iternodes()):
if not n.isleaf:
n.label = "node%s" % i
node.label = "root"
n2c = calc_node_positions(node, radius=100, scaled=False)
from matplotlib.patches import Arc, PathPatch
from matplotlib.collections import PatchCollection, LineCollection
import matplotlib.pyplot as P
f = P.figure()
a = f.add_subplot(111)
arcs = []; lines = []
for n in node.iternodes():
c = n2c[n]
if n.parent and n.children:
theta1 = n2c[n.children[0]].angle
theta2 = n2c[n.children[-1]].angle
arc = Arc((0,0), c.depth*2, c.depth*2, theta1=theta1, theta2=theta2)
arcs.append(arc)
if n.parent:
p = n2c[n.parent]
px = math.cos(math.radians(c.angle))*p.depth
py = math.sin(math.radians(c.angle))*p.depth
lines.append(((c.x,c.y),(px, py)))
if n.label:
txt = a.annotate(
n.label,
xy=(c.x, c.y),
xytext=(0, 0),
textcoords="offset points"
)
arcs = PatchCollection(arcs, match_original=True)
a.add_collection(arcs)
lines = LineCollection(lines)
a.add_collection(lines)
a.set_xlim((-100,100))
a.set_ylim((-100,100))
f.show()
def test_brownian():
"""
Evolve a trait up an example tree of primates:.
((((H**o:0.21,Pongo:0.21)N1:0.28,Macaca:0.49)N2:0.13,
Ateles:0.62)N3:0.38,Galago:1.00)root;
Returns: (*root*, *data*) - the root node and evolved data.
"""
import newick
root = newick.parse(
"((((H**o:0.21,Pongo:0.21)N1:0.28,Macaca:0.49)N2:0.13,"\
"Ateles:0.62)N3:0.38,Galago:1.00)root;"
)
print(root.ascii(scaled=True))
evolved = brownian(root)
for node in root.iternodes():
print(node.label, evolved[node])
return root, evolved
import newick, tree, cyexpokit
import numpy as np
s = '((((H**o:0.21,Pongo:0.21)A:0.28,Macaca:0.49)B:0.13,Ateles:0.62)C:0.38,Galago:1.00)root;'
r = newick.parse(s)
t = tree.Tree(r)
data = dict(zip(t.leaf_labels(), [1,0,0,0,0]))
qidx = np.array([[0,0,1,0],
[0,1,0,0]])
f = cyexpokit.make_mklnl_func(t, data, 2, 1, qidx)
v = []
n = newroot
while 1:
v.append(n)
if not n.parent: break
n = n.parent
#print [ x.label for x in v ]
v.reverse()
for i, cp in enumerate(v[:-1]):
node = v[i+1]
# node is current node; cp is current parent
#print node.label, cp.label
cp.remove_child(node)
node.add_child(cp)
cp.length = node.length
return newroot
if __name__ == "__main__":
import newick, ascii, os
from numpy import array
#tree = newick.parse("(a,(b,(c,(d,e))));")
f = os.path.expanduser("~/Projects/pedic-sympatry/matrices/")
tree = eval(file(f+"garli-ml.tree").read())
treespp = tree["species"]
root = newick.parse(tree["newick"])
spp = ['alaschanica', 'cheilanthifolia', 'dichotoma', 'kansuensis',
'oederi', 'plicata', 'przewalskii', 'remotiloba',
'rhinanthoides', 'roylei', 'rupicola', 'scolopax']
print root.subtree_mapping(spp, clean=1)
if node.label and show_internal_labels:
label = node2label[node]
buf.putstr(node.r, node.c - len(label), label)
buf.putstr(node.r, node.c, "+")
return str(buf)
render = tree2ascii
if __name__ == "__main__":
import random
rand = random.Random()
t = newick.parse("(foo,((bar,(dog,cat)),(shoe,(fly,(cow, bowwow)))));")
t = newick.parse("(((foo:4.6):5.6, (bar:6.5, baz:2.3):3.0):3.0);")
data = {"foo": 1, "bar": 0, "baz": 1}
#print t, t.next.back, t.next.next.back, t.next.next.next.back,
## print t, t.next, t.next.next, t.next.next.next
## print t.fnodes()
# sys.exit()
i = 1
for n in t.iternodes():
#n.length = rand.random()
if not n.istip:
n.label = "n%s" % i
i += 1
print tree2ascii(t, scaled=1, show_internal_labels=0, data=data)
while 1:
v.append(n)
if not n.parent: break
n = n.parent
#print [ x.label for x in v ]
v.reverse()
for i, cp in enumerate(v[:-1]):
node = v[i + 1]
# node is current node; cp is current parent
#print node.label, cp.label
cp.remove_child(node)
node.add_child(cp)
cp.length = node.length
return newroot
if __name__ == "__main__":
import newick, ascii, os
from numpy import array
#tree = newick.parse("(a,(b,(c,(d,e))));")
f = os.path.expanduser("~/Projects/pedic-sympatry/matrices/")
tree = eval(file(f + "garli-ml.tree").read())
treespp = tree["species"]
root = newick.parse(tree["newick"])
spp = [
'alaschanica', 'cheilanthifolia', 'dichotoma', 'kansuensis', 'oederi',
'plicata', 'przewalskii', 'remotiloba', 'rhinanthoides', 'roylei',
'rupicola', 'scolopax'
]
print root.subtree_mapping(spp, clean=1)
import newick, mcmc
r = newick.parse(open('/home/rree/src/ivy/examples/primates.newick').read())
mcmc.insert_knees(r)
def read(data, format=None, treename=None, ttable=None):
"""
Read a single tree from *data*, which can be a Newick string, a
file name, or a file-like object with `tell` and 'read`
methods. *treename* is an optional string that will be attached to
all created nodes.
Args:
data: A file or file-like object or newick string
Returns:
Node: The root node.
"""
import newick
StringTypes = types.StringTypes
def strip(s):
fname = os.path.split(s)[-1]
head, tail = os.path.splitext(fname)
tail = tail.lower()
if tail in (".nwk", ".tre", ".tree", ".newick", ".nex"):
return head
else:
return fname
if (not format):
if (type(data) in StringTypes) and os.path.isfile(data):
s = data.lower()
for tail in ".nex", ".nexus", ".tre":
if s.endswith(tail):
format="nexus"
break
if (not format):
format = "newick"
if format == "newick":
if type(data) in StringTypes:
if os.path.isfile(data):
treename = strip(data)
return newick.parse(file(data), treename=treename,
ttable=ttable)
else:
return newick.parse(data, ttable=ttable)
elif (hasattr(data, "tell") and hasattr(data, "read")):
treename = strip(getattr(data, "name", None))
return newick.parse(data, treename=treename, ttable=ttable)
elif format == "nexus-dendropy":
import dendropy
if type(data) in StringTypes:
if os.path.isfile(data):
treename = strip(data)
return newick.parse(
str(dendropy.Tree.get_from_path(data, "nexus")),
treename=treename
)
else:
return newick.parse(
str(dendropy.Tree.get_from_string(data, "nexus"))
)
elif (hasattr(data, "tell") and hasattr(data, "read")):
treename = strip(getattr(data, "name", None))
return newick.parse(
str(dendropy.Tree.get_from_stream(data, "nexus")),
treename=treename
)
else:
pass
elif format == "nexus":
if type(data) in StringTypes:
if os.path.isfile(data):
with open(data) as infile:
rec = newick.nexus_iter(infile).next()
if rec: return rec.parse()
else:
rec = newick.nexus_iter(StringIO(data)).next()
if rec: return rec.parse()
else:
rec = newick.nexus_iter(data).next()
if rec: return rec.parse()
else:
# implement other tree formats here (nexus, nexml etc.)
raise IOError, "format '%s' not implemented yet" % format
raise IOError, "unable to read tree from '%s'" % data
import tempfile, commands, os, sys
fname = tempfile.mktemp(suffix=".svg")
svg = fig.SVG()
vb = "%s %s %s %s" % (0, 0, w, h)
svgfig.canvas(svg, width=w, height=h, viewBox=vb).save(fname)
#svg.save(fname)
width = float(commands.getoutput("inkscape -W '%s'" % fname))
height = float(commands.getoutput("inkscape -H '%s'" % fname))
os.remove(fname)
return width, height
w = 400.0
h = 800.0
r = newick.parse(file("test.newick").read())
r.order_subtrees_by_size()
n2c = layout.calc_node_positions(r, w, h, scaled=True)
ntips = float(len(r.leaves()))
fontsize = h / ntips
## bbox = svgfig.Rect(1,1,w-1,h-1)
branches = []
labels = []
for n, c in n2c.items():
if n.parent:
pc = n2c[n.parent]
d = ((c.x, c.y), (pc.x, c.y), (pc.x, pc.y))
line = svgfig.Poly(d)
branches.append(line)
#print n.label, c.x, c.y
if not scaled:
for i in range(10):
smooth_xpos(node, n2coords, collapsed=collapsed)
for coords in n2coords.values():
coords.x += lpad
coords.y += tpad
for n, coords in n2coords.items():
if n.parent:
p = n2coords[n.parent]
coords.px = p.x
coords.py = p.y
else:
coords.px = None
coords.py = None
return n2coords
if __name__ == "__main__":
import newick
node = newick.parse("(a:3,(b:2,(c:4,d:5):1,(e:3,(f:1,g:1):2):2):2);")
for i, n in enumerate(node.iternodes()):
if not n.istip:
n.label = "node%s" % i
node.label = "root"
calc_node_positions(node, width=10, height=10, scaled=True)
leaf_indices = list(RandomArray.permutation(len(leaves)))
joined = [leaves[leaf_indices.pop()]]
remaining = leaf_indices
while remaining:
i = RandomArray.randint(0, len(joined)-1)
c1 = joined[i]
if c1.back:
n = c1.bisect()
else:
n = InternalNode()
n.add_child(c1)
c = leaves[remaining.pop()]
n.add_child(c)
joined.append(c)
joined.append(n)
for node in joined:
if not node.back:
node.isroot = 1
return node
if __name__ == "__main__":
import newick
tree = newick.parse("(a,(b,(c,(d,e))));")
for i, n in enumerate(tree.descendants(order=PREORDER)):
print i, n.label or n
#print tree.draw_ascii
def get_input_tree(infile, opts=None):
pos = infile.tell()
line = infile.readline()
infile.seek(pos)
if line.upper().startswith("#NEXUS"):
newick_trees = get_trees_from_nexus(infile)
else:
if opts.dsdn:
opts.S, opts.N = map(float, infile.readline().split())
newick_trees = infile.read().split(";")
tree = newick.parse(newick_trees[0])
## reroot(tree, ["ptheirospermum_tenuisec_28207", "seymeria_pectinata"])
node, mapping = traverse(tree)
node.sort()
if opts.dsdn:
def func(n):
try:
n.dS = n.length
n.length = None
except AttributeError: pass
node.foreach(func)
dN_newick = newick_trees[1].strip()
assert dN_newick
dN = newick.parse(dN_newick)
labelset2treenode = tree_compare.set_labels(tree)
labelset2dNnode = tree_compare.set_labels(dN)
for labelset, dNnode in labelset2dNnode.items():
treenode = labelset2treenode.get(labelset)
if treenode:
try:
gnode = mapping[treenode]
gnode.dN = dNnode.length
## gnode.dsdn = "%0.1f/%0.1f" % (gnode.dS*opts.S,
## gnode.dN*opts.N)
try:
if gnode.dN > 0.0:
gnode.dsdn = "%f" % (gnode.dN/gnode.dS)
else:
gnode.dsdn = ""
except ZeroDivisionError:
gnode.dsdn = ""
except KeyError:
pass
return node
try:
support_newick = newick_trees[1].strip()
if support_newick:
support = newick.parse(support_newick)
labelset2treenode = tree_compare.set_labels(tree)
labelset2supportnode = tree_compare.set_labels(support)
for labelset, supportnode in labelset2supportnode.items():
treenode = labelset2treenode.get(labelset)
if treenode:
try:
gnode = mapping[treenode]
gnode.support = supportnode.length
except KeyError:
pass
except IndexError:
pass
# add parsing for other file formats here
return node
def __init__(self, newickstr, periods=None, root_age=None):
"""
newickstr: newick tree with branch lengths
periods: list of durations ordered from present to past
root_age: age of root node for branch length scaling
"""
self.root = newick.parse(newickstr)
self.newick = newickstr
#phylo.polarize(self.root)
self.periods = periods
# initialize nodes (label interiors, etc)
# and collect leaves and postorder sequence
self.postorder_nodes = []
self.leaves = []
#for i, node in enumerate(self.root.descendants(phylo.POSTORDER)):
polytomies = []
for i, node in enumerate(self.root.iternodes(phylo.POSTORDER)):
node.tree = self
node.number = i
node.segments = []
if (not node.istip) and (not node.label):
node.label = "N%s" % node.number
node.age = None
if node.istip:
#node.age = 0.0
self.leaves.append(node)
else:
#nc = len(node.children())
nc = node.nchildren
if nc > 2:
polytomies.append((nc, node.label))
## if nc > 2:
## print ascii.tree2ascii(self.root)
## assert nc == 2, \
## "%s-way polytomy at node %s" % (nc, node.label)
self.postorder_nodes.append(node)
if polytomies:
msg = []
msg.append(", ".join([ "%s-way polytomy at node %s" % (nc, label) \
for nc, label in polytomies ]))
## msg.append("Tree is:")
## msg.append(ascii.tree2ascii(self.root))
#print "\n".join(msg)
raise Error, "\n".join(msg)
self.root_age = root_age
if root_age:
self.calibrate(root_age)
self.label2node = dict([(n.label, n) for n in self.postorder_nodes])
for node in self.postorder_nodes:
if node.parent:
if not (node.length > 0):
print >> sys.stderr, \
"Warning: node %s: "\
"changing branch length of %s to %g" \
% (node.label, node.length, SHORT)
node.length = SHORT
self.assign_node_ages()
## for node in self.postorder_nodes:
## if node.parent and (node.parent.age is None):
## node.parent.age = node.age + node.length
# initialize branch segments
for node in self.postorder_nodes:
if node.parent:
periods = self.periods
anc = node.parent.age
des = node.age
assert anc > des, "%s = %g, %s = %g\n%s" \
% (node.parent.label, anc, node.label, des,
self.root.render_ascii(scaled=1, minwidth=80))
t = des
if periods:
for i, p in enumerate(periods):
s = sum(periods[:i + 1])
if t < s:
duration = min((s - t, anc - t))
if duration > 0:
seg = BranchSegment(duration, i)
node.segments.append(seg)
#t += p
t += duration
if t > anc:
break
else:
node.segments = [BranchSegment(node.length, 0)]
else:
if node.label and show_internal_labels:
label = node2label[node]
buf.putstr(node.r, node.c-len(label), label)
buf.putstr(node.r, node.c, "+")
return str(buf)
render = tree2ascii
if __name__ == "__main__":
import random
rand = random.Random()
t = newick.parse("(foo,((bar,(dog,cat)),(shoe,(fly,(cow, bowwow)))));")
t = newick.parse("(((foo:4.6):5.6, (bar:6.5, baz:2.3):3.0):3.0);")
data = {"foo":1, "bar":0, "baz":1}
#print t, t.next.back, t.next.next.back, t.next.next.next.back,
## print t, t.next, t.next.next, t.next.next.next
## print t.fnodes()
# sys.exit()
i = 1
for n in t.iternodes():
#n.length = rand.random()
if not n.istip:
n.label = "n%s" % i
i += 1
print tree2ascii(t, scaled=1, show_internal_labels=0, data=data)
else:
if node.label and show_internal_labels:
buf.putstr(node.r, node.c - len(node.label), node.label)
buf.putstr(node.r, node.c, "+")
return str(buf)
render = tree2ascii
if __name__ == "__main__":
import random
rand = random.Random()
t = newick.parse(
"(foo,((bar,(dog,cat)dc)dcb,(shoe,(fly,(cow, bowwow)cowb)cbf)X)Y)Z;")
#t = newick.parse("(((foo:4.6):5.6, (bar:6.5, baz:2.3):3.0):3.0);")
#t = newick.parse("(foo:4.6, (bar:6.5, baz:2.3)X:3.0)Y:3.0;")
i = 1
## for n in t.descendants():
## #n.length = rand.random()
## if not n.istip:
## n.label = "n%s" % i
## print n, n.label
## i += 1
print tree2ascii(t, scaled=0, show_internal_labels=1)
r = t.find_descendant("cat").parent
phylo.reroot(t, r)
tp = t.parent
tp.remove_child(t)
def parse(self, newick=newick):
assert self.newick
self.root = newick.parse(
self.newick, ttable=self.ttable, treename=self.name
)
return self.root
# make the new age the average of parent and max child
new_node_age = (parent_age + max_child_age)/2.0
results[node] = new_node_age
else:
results[node] = node_ages[node]
else:
results[node] = node_ages[node]
for child in node.children:
smooth(child, node_ages, results)
return results
if __name__ == "__main__":
import newick, ascii
s = "((((a,b),(c,d),(e,f)),g),h);"
root = newick.parse(s)
leaf_ages = {
"a": 3,
"b": 2,
"c": 4,
"d": 1,
"e": 3,
"f": 0.5,
"g": 10,
"h": 5,
}
ma = min_ages(root, leaf_ages)
d = ma
for i in range(10):
c.x = c.length_to_root * scale
for n in node.iternodes(phylo.POSTORDER):
c = n2coords[n]
if not n.istip:
children = n.children
ymax = n2coords[children[0]].y
ymin = n2coords[children[-1]].y
c.y = (ymax + ymin)/2.0
if not scaled:
c.x = min([ n2coords[ch].x for ch in children ]) - unitwidth
else:
c.x = c.length_to_root * scale
#print n.label, c.x, c.y
if not scaled:
for i in range(10):
smooth_xpos(node, n2coords)
return n2coords
if __name__ == "__main__":
import newick
node = newick.parse("(a:3,(b:2,(c:4,d:5):1,(e:3,(f:1,g:1):2):2):2);")
for i, n in enumerate(node.iternodes()):
if not n.istip:
n.label = "node%s" % i
node.label = "root"
calc_node_positions(node, width=10, height=10, scaled=True)
import newick, cy_tree import numpy as np s = '((((H**o:0.21,Pongo:0.21)A:0.28,Macaca:0.49)B:0.13,Ateles:0.62)C:0.38,Galago:1.00)root;' r = newick.parse(s) t = cy_tree.Tree(r) a = np.empty(t.nnodes, dtype=int) cy_tree.cladesizes3(t, a) print a
def get_input_tree(infile, opts=None):
pos = infile.tell()
line = infile.readline()
infile.seek(pos)
if line.upper().startswith("#NEXUS"):
newick_trees = get_trees_from_nexus(infile)
else:
if opts.dsdn:
opts.S, opts.N = map(float, infile.readline().split())
newick_trees = infile.read().split(";")
tree = newick.parse(newick_trees[0])
## reroot(tree, ["ptheirospermum_tenuisec_28207", "seymeria_pectinata"])
node, mapping = traverse(tree)
node.sort()
if opts.dsdn:
def func(n):
try:
n.dS = n.length
n.length = None
except AttributeError:
pass
node.foreach(func)
dN_newick = newick_trees[1].strip()
assert dN_newick
dN = newick.parse(dN_newick)
labelset2treenode = tree_compare.set_labels(tree)
labelset2dNnode = tree_compare.set_labels(dN)
for labelset, dNnode in labelset2dNnode.items():
treenode = labelset2treenode.get(labelset)
if treenode:
try:
gnode = mapping[treenode]
gnode.dN = dNnode.length
## gnode.dsdn = "%0.1f/%0.1f" % (gnode.dS*opts.S,
## gnode.dN*opts.N)
try:
if gnode.dN > 0.0:
gnode.dsdn = "%f" % (gnode.dN / gnode.dS)
else:
gnode.dsdn = ""
except ZeroDivisionError:
gnode.dsdn = ""
except KeyError:
pass
return node
try:
support_newick = newick_trees[1].strip()
if support_newick:
support = newick.parse(support_newick)
labelset2treenode = tree_compare.set_labels(tree)
labelset2supportnode = tree_compare.set_labels(support)
for labelset, supportnode in labelset2supportnode.items():
treenode = labelset2treenode.get(labelset)
if treenode:
try:
gnode = mapping[treenode]
gnode.support = supportnode.length
except KeyError:
pass
except IndexError:
pass
# add parsing for other file formats here
return node
def __init__(self, newickstr, periods=None, root_age=None):
"""
newickstr: newick tree with branch lengths
periods: list of durations ordered from present to past
root_age: age of root node for branch length scaling
"""
self.root = newick.parse(newickstr)
self.newick = newickstr
#phylo.polarize(self.root)
self.periods = periods
# initialize nodes (label interiors, etc)
# and collect leaves and postorder sequence
self.postorder_nodes = []
self.leaves = []
#for i, node in enumerate(self.root.descendants(phylo.POSTORDER)):
polytomies = []
for i, node in enumerate(self.root.iternodes(phylo.POSTORDER)):
node.tree = self
node.number = i
node.segments = []
if (not node.istip) and (not node.label):
node.label = "N%s" % node.number
node.age = None
if node.istip:
#node.age = 0.0
self.leaves.append(node)
else:
#nc = len(node.children())
nc = node.nchildren
if nc > 2:
polytomies.append((nc, node.label))
## if nc > 2:
## print ascii.tree2ascii(self.root)
## assert nc == 2, \
## "%s-way polytomy at node %s" % (nc, node.label)
self.postorder_nodes.append(node)
if polytomies:
msg = []
msg.append(", ".join([ "%s-way polytomy at node %s" % (nc, label) \
for nc, label in polytomies ]))
## msg.append("Tree is:")
## msg.append(ascii.tree2ascii(self.root))
#print "\n".join(msg)
raise Error("\n".join(msg))
self.root_age = root_age
if root_age:
self.calibrate(root_age)
self.label2node = dict([(n.label, n) for n in self.postorder_nodes ])
for node in self.postorder_nodes:
if node.parent:
if not (node.length > 0):
print("Warning: node %s: "\
"changing branch length of %s to %g" \
% (node.label, node.length, SHORT), file=sys.stderr)
node.length = SHORT
self.assign_node_ages()
## for node in self.postorder_nodes:
## if node.parent and (node.parent.age is None):
## node.parent.age = node.age + node.length
# initialize branch segments
for node in self.postorder_nodes:
if node.parent:
periods = self.periods
anc = node.parent.age
des = node.age
assert anc > des, "%s = %g, %s = %g\n%s" \
% (node.parent.label, anc, node.label, des,
self.root.render_ascii(scaled=1, minwidth=80))
t = des
if periods:
for i, p in enumerate(periods):
s = sum(periods[:i+1])
if t < s:
duration = min((s - t, anc - t))
if duration > 0:
seg = BranchSegment(duration, i)
node.segments.append(seg)
#t += p
t += duration
if t > anc:
break
else:
node.segments = [BranchSegment(node.length, 0)]
"use inkscape to calculate the width and height of fig"
import tempfile, commands, os, sys
fname = tempfile.mktemp(suffix=".svg")
svg = fig.SVG()
vb = "%s %s %s %s" % (0, 0, w, h)
svgfig.canvas(svg, width=w, height=h, viewBox=vb).save(fname)
#svg.save(fname)
width = float(commands.getoutput("inkscape -W '%s'" % fname))
height = float(commands.getoutput("inkscape -H '%s'" % fname))
os.remove(fname)
return width, height
w = 400.0
h = 800.0
r = newick.parse(file("test.newick").read())
r.order_subtrees_by_size()
n2c = layout.calc_node_positions(r, w, h, scaled=True)
ntips = float(len(r.leaves()))
fontsize = h/ntips
## bbox = svgfig.Rect(1,1,w-1,h-1)
branches = []
labels = []
for n, c in n2c.items():
if n.parent:
pc = n2c[n.parent]
d = ((c.x, c.y), (pc.x, c.y), (pc.x, pc.y))
line = svgfig.Poly(d)
branches.append(line)
new_node_age = (parent_age + max_child_age) / 2.0
results[node] = new_node_age
else:
results[node] = node_ages[node]
else:
results[node] = node_ages[node]
for child in node.children:
smooth(child, node_ages, results)
return results
if __name__ == "__main__":
import newick, ascii
s = "((((a,b),(c,d),(e,f)),g),h);"
root = newick.parse(s)
leaf_ages = {
"a": 3,
"b": 2,
"c": 4,
"d": 1,
"e": 3,
"f": 0.5,
"g": 10,
"h": 5,
}
ma = min_ages(root, leaf_ages)
d = ma
for i in range(10):
buf.putstr(node.r, node.c+1, " "+node.label)
else:
if node.label and show_internal_labels:
buf.putstr(node.r, node.c-len(node.label), node.label)
buf.putstr(node.r, node.c, "+")
return str(buf)
render = tree2ascii
if __name__ == "__main__":
import random
rand = random.Random()
t = newick.parse("(foo,((bar,(dog,cat)dc)dcb,(shoe,(fly,(cow, bowwow)cowb)cbf)X)Y)Z;")
#t = newick.parse("(((foo:4.6):5.6, (bar:6.5, baz:2.3):3.0):3.0);")
#t = newick.parse("(foo:4.6, (bar:6.5, baz:2.3)X:3.0)Y:3.0;")
i = 1
## for n in t.descendants():
## #n.length = rand.random()
## if not n.istip:
## n.label = "n%s" % i
## print n, n.label
## i += 1
print tree2ascii(t, scaled=0, show_internal_labels=1)
r = t.find_descendant("cat").parent
phylo.reroot(t, r)
tp = t.parent
tp.remove_child(t)
