def upload_newick():
#n = "_".join(request.vars.name.strip().split())
n = None
age = request.vars.age.strip()
if age:
try:
age = float(age)
except:
session.flash = "Age must be a number"
s = request.vars.newick_string.strip()
if s:
r = None
try:
r = newick.parse(s)
except:
session.flash = "Problem with newick string"
if r:
m = current_model()
m.treelist.append(s, name=n, age=age)
t = m.treelist.trees[-1]
t.parse()
if not t.scaled:
for n in t.root.iternodes():
if n.parent and (n.length is None):
n.length = 1
t.calibrate()
t.scaled = True
t.newick = newick.tostring(t.root)+";"
session.flash = "Branches without lengths assigned a value of 1"
if not t.is_ultrametric():
session.flash = "Tree is not ultrametric"
redirect(URL(r=request, f=request.vars.f or "index"))
def upload_newick():
#n = "_".join(request.vars.name.strip().split())
n = None
age = request.vars.age.strip()
if age:
try:
age = float(age)
except:
session.flash = "Age must be a number"
s = request.vars.newick_string.strip()
if s:
r = None
try:
r = newick.parse(s)
except:
session.flash = "Problem with newick string"
if r:
m = current_model()
m.treelist.append(s, name=n, age=age)
t = m.treelist.trees[-1]
t.parse()
if not t.scaled:
for n in t.root.iternodes():
if n.parent and (n.length is None):
n.length = 1
t.calibrate()
t.scaled = True
t.newick = newick.tostring(t.root) + ";"
session.flash = "Branches without lengths assigned a value of 1"
if not t.is_ultrametric():
session.flash = "Tree is not ultrametric"
redirect(URL(r=request, f=request.vars.f or "index"))
def parse(self, s=None):
if s:
self.newick = s
self.root = newick.parse(self.newick)
scaled = True
for i, n in enumerate(self.root.iternodes(phylo.POSTORDER)):
n.number = i
if (not n.istip) and (not n.label):
n.label = "N%s" % n.number
n.age = None
if n.parent and (n.length is None):
scaled = False
if scaled:
for i, n in enumerate(self.root.iternodes(phylo.POSTORDER)):
if n.length == 0:
n.length = 1e-05
self.newick = newick.tostring(self.root) + ";"
self.scaled = scaled
def parse(self, s=None):
if s:
self.newick = s
self.root = newick.parse(self.newick)
scaled = True
for i, n in enumerate(self.root.iternodes(phylo.POSTORDER)):
n.number = i
if (not n.istip) and (not n.label):
n.label = "N%s" % n.number
n.age = None
if n.parent and (n.length is None):
scaled = False
if scaled:
for i, n in enumerate(self.root.iternodes(phylo.POSTORDER)):
if n.length == 0:
n.length = 1e-05
self.newick = newick.tostring(self.root)+";"
self.scaled = scaled
