def my_tree_loader(tree):
""" This function is used to load trees within the WebTreeApplication object. """
t = PhyloTree(tree, sp_naming_function=None)
#Check one leaf to see if species information is included
if t.get_leaves()[0].species == "Unknown":
t.set_species_naming_function(extract_species_code)
return t
def main():
fn=sys.argv[1]
nw=open(fn).readline()
species={}
t=PhyloTree(nw)
#set species naming function
t.set_species_naming_function(_get_spcode)
for l in t.get_leaves():
spCode=l.species
try: species[spCode]+=1
except: species[spCode] =1
for spCode in sorted( species, key=lambda x: species[x], reverse=True ):
print '%s\t%s' % ( spCode,species[spCode] )
def main():
fn = sys.argv[1]
nw = open(fn).readline()
species = {}
t = PhyloTree(nw)
#set species naming function
t.set_species_naming_function(_get_spcode)
for l in t.get_leaves():
spCode = l.species
try:
species[spCode] += 1
except:
species[spCode] = 1
for spCode in sorted(species, key=lambda x: species[x], reverse=True):
print '%s\t%s' % (spCode, species[spCode])
t = PhyloTree("(((Hsa_001,Ptr_001),(Cfa_001,Mms_001)),(Dme_001,Dme_002));")
# /-Hsa_001
# /--------|
# | \-Ptr_001
# /--------|
# | | /-Cfa_001
# | \--------|
#---------| \-Mms_001
# |
# | /-Dme_001
# \--------|
# \-Dme_002
#
# Prints current leaf names and species codes
print "Deafult mode:"
for n in t.get_leaves():
print "node:", n.name, "Species name:", n.species
# node: Dme_001 Species name: Dme
# node: Dme_002 Species name: Dme
# node: Hsa_001 Species name: Hsa
# node: Ptr_001 Species name: Ptr
# node: Cfa_001 Species name: Cfa
# node: Mms_001 Species name: Mms
#
# We can also use our own leaf name parsing function to obtain species
# names. All we need to do is create a python function that takes
# node's name as argument and return its corresponding species name.
def get_species_name(node_name_string):
# Species code is the first part of leaf name (separated by an
# underscore character)
spcode = node_name_string.split("_")[0]
