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 ascii_tree(outfile, tree, model, data=None, scaled=False, minwidth=80,
tee=False):
d = None
if data:
d = dict([ (x[0], model.dist2label(x[1])) for x in data.items() \
if x[1] in model.dists ])
s = "\n".join(
["Newick tree with interior nodes labeled:",
newick.to_string(tree.root)+";", "\n",
"Cladogram (branch lengths not to scale):",
ascii.render(tree.root, scaled=scaled, minwidth=80, data=d),
"\n\n"]
)
log(s, outfile, tee)
def ascii(self, *args, **kwargs):
"""
Create ascii tree.
Keyword Args:
unitlen (float): How long each unit should be rendered as.
Defaults to 3.
minwidth (float): Minimum width of the plot. Defaults to 50
maxwidth (float): Maximum width of the plot. Defaults to None
scaled (bool): Whether or not the tree is scaled. Defaults to False
show_internal_labels (bool): Whether or not to show labels
on internal nodes. Defaults to True.
Returns:
str: Ascii tree to be shown with print().
"""
from ascii import render
return render(self, *args, **kwargs)
i += 1
return root
def ultrametricize(node):
import layout
n2c = layout.calc_node_positions(node, 1.0, 1.0, scaled=False)
for n in node.descendants():
c = n2c[n]
n.length = c.x - n2c[n.parent].x
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)
root = bifid_tree(5)
ultrametricize(root)
print newick.tostring(root)
print ascii.render(root)
#print node2tipsets(root)
print root.mrca(("SP6", "SP10", "SP18")).label
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):
d = smooth(root, d)
for node, val in ages2lengths(root, d).items():
node.length = val
print(ascii.render(root, scaled=1))
def ascii(self, *args, **kwargs):
from ascii import render
return render(self, *args, **kwargs)
## N = len(labels)
## var = [ [ 0 for x in labels ] for y in labels ]
## cov = [ [ None for x in labels ] for y in labels ]
## d = root.leaf_distances()
## for i in range(N):
## for j in range(i+1, N):
## li = labels[i]
## lj = labels[j]
## for n in root.postiter():
## l2d = d[n]
## if (not n.isleaf) and (li in l2d) and (lj in l2d):
## dist = l2d[li] + l2d[lj]
## var[i][j] = dist
## cov[i][j] = sum([ x.length for x in n.rootpath()
## if x.parent ])
## break
## return var, cov
if __name__ == "__main__":
import tree, ascii
from pprint import pprint
n = tree.read("(((a:1,b:2):3,(c:3,d:1):1,(e:0.5,f:3):2.5):1,g:4);")
var, covar = vcv(n)
for x in n:
if not x.label: x.label = str(x.length or "")
else: x.label = "%s %s" % (x.length, x.label)
print ascii.render(n, scaled=1)
for k, v in var.items():
print [ x.label.split()[-1] for x in k ], v, covar[k]
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):
d = smooth(root, d)
for node, val in ages2lengths(root, d).items():
node.length = val
print ascii.render(root, scaled=1)
def ascii(self, *args, **kwargs):
from ascii import render
return render(self, *args, **kwargs)
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):
d = smooth(root, d)
for node, val in ages2lengths(root, d).items():
node.length = val
print ascii.render(root, scaled=1)
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):
d = smooth(root, d)
for node, val in ages2lengths(root, d).items():
node.length = val
print(ascii.render(root, scaled=1))
else:
n.label = "IN%s" % i
i += 1
return root
def ultrametricize(node):
import layout
n2c = layout.calc_node_positions(node, 1.0, 1.0, scaled=False)
for n in node.descendants():
c = n2c[n]
n.length = c.x - n2c[n.parent].x
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)
root = bifid_tree(5)
ultrametricize(root)
print newick.tostring(root)
print ascii.render(root)
#print node2tipsets(root)
print root.mrca(("SP6","SP10", "SP18")).label
# Xk is the reconstructed state at the node
Xk = ((1.0/vi)*Xi + (1/vj)*Xj) / (1.0/vi + 1.0/vj)
# vk is the variance
vk = node.length + (vi*vj)/(vi+vj)
results[node] = (Xk, vk, Xi-Xj, vi+vj)
return results
if __name__ == "__main__":
import tree
n = tree.read(
"((((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)N4:0.0;"
)
char1 = {
"H**o": 4.09434,
"Pongo": 3.61092,
"Macaca": 2.37024,
"Ateles": 2.02815,
"Galago": -1.46968
}
for k, v in PIC(n, char1).items():
print k.label or k.id, v
import ascii
print ascii.render(n, scaled=True)
# Xk is the reconstructed state at the node
Xk = ((1.0 / vi) * Xi + (1 / vj) * Xj) / (1.0 / vi + 1.0 / vj)
# vk is the variance
vk = node.length + (vi * vj) / (vi + vj)
results[node] = (Xk, vk, Xi - Xj, vi + vj)
return results
if __name__ == "__main__":
import tree
n = tree.read(
"((((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)N4:0.0;"
)
char1 = {
"H**o": 4.09434,
"Pongo": 3.61092,
"Macaca": 2.37024,
"Ateles": 2.02815,
"Galago": -1.46968
}
for k, v in PIC(n, char1).items():
print k.label or k.id, v
import ascii
print ascii.render(n, scaled=True)
## for child in children:
## nstr = nstr+to_string(child, lengths)
## if child != children[-1]: nstr = nstr+','
## nstr = nstr+')'
## else:
## label = node.label
## nstr = nstr+label
## if (node.length is not None) and lengths:
## nstr = nstr+':'+'%f' % node.length
## return nstr
def parse_from_file(filename):
if filename == '-':
file = sys.stdin
else:
file = open(filename, 'r')
content = string.strip(file.read())
treedescs = string.split(content, ';')
tree = parse(treedescs[0])
file.close()
return tree
if __name__ == "__main__":
import ascii
s = "(a,(b,c)int)root;"
n = parse(s)
print
print ascii.render(n)
print to_string(n)
print n.next.back.label