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])
'28': 'HR2',
'30': 'G11012',
'24': 'Pm1'
}
# for i in range(len(nos)):
# dt[nos[i]] = dataorder[i]
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
# We could even translate the code to complete names
code2name = dt
return code2name[spcode]
t.set_species_naming_function(get_species_name)
for node in t.iter_search_nodes():
if node.name == "43":
node.dist = 5e-05
#t.show(tree_style=ts)
# t.render("/Volumes/MP_HD/CI_GENOME_SEQ/CI_gene_coverage (generate stat for sig diff cov)/gene_copy_no_tree/CI_gain_loss_tree.pdf",tree_style=ts,w=3200,h=4800,dpi=200)
t.render(
"/Volumes/MP_HD/CI_GENOME_SEQ/CI_orthomcl_data/gain_loss_tree_frm_orthogroups/CI_denovo_gene_gain_loss_tree.pdf",
tree_style=ts,
w=3200,
h=4800,
dpi=200)
# 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]
# We could even translate the code to complete names
code2name = {
"Dme":"Drosophila melanogaster",
"Hsa":"H**o sapiens",
"Ptr":"Pan troglodytes",
"Mms":"Mus musculus",
"Cfa":"Canis familiaris"
}
return code2name[spcode]
# Now, let's ask the tree to use our custom species naming function
t.set_species_naming_function(get_species_name)
print "Custom mode:"
for n in t.get_leaves():
print "node:", n.name, "Species name:", n.species
# node: Dme_001 Species name: Drosophila melanogaster
# node: Dme_002 Species name: Drosophila melanogaster
# node: Hsa_001 Species name: H**o sapiens
# node: Ptr_001 Species name: Pan troglodytes
# node: Cfa_001 Species name: Canis familiaris
# node: Mms_001 Species name: Mus musculus
#
# Of course, you can disable the automatic generation of species
# names. To do so, you can set the species naming function to
# None. This is useful to set the species names manually or for
# reading them from a newick file. Other wise, species attribute would
# be overwriten
