def _build_tree(self, tree_file, tree_format):
if tree_format == 'newick_string':
self.tree_str = tree_file
return ete3.Tree(self.tree_str, format=1)
elif tree_format == 'newick':
with open(tree_file, 'r') as nwk_file:
self.tree_str = nwk_file.read()
return ete3.Tree(self.tree_str, format=1)
elif tree_format == 'phyloxml':
from ete3 import Phyloxml
project = Phyloxml()
project.build_from_file(tree_file)
self.tree_str = None
tree = project.get_phylogeny()[0]
for node in tree.traverse():
# assign name to extant species
if node.is_leaf():
node.name = self._get_name_phyloxml(
node, self.phyloxml_leaf_name_tag)
# assign name to ancestral species
elif self.use_internal_name:
node.name = self._get_name_phyloxml(
node, self.phyloxml_internal_name_tag)
return tree
def getTreeFromPhyloxml(xml, saveToFile="default.xml", delFile=True):
"""
Read a phylogeny tree from a phyloxml string and return a TreeClass object
or a list of TreeClass object
"""
project = Phyloxml()
fo = open(saveToFile, "w+")
fo.write(xml)
fo.close()
project.build_from_file(saveToFile)
treeList = []
for tree in project.get_phylogeny():
treeList.append(TreeClass.import_from_PhyloxmlTree(tree))
if (delFile):
os.remove(saveToFile)
if len(treeList) == 1:
return treeList[0]
return treeList
def getTreeFromPhyloxml(xml, saveToFile="default.xml", delFile=True):
"""
Read a phylogeny tree from a phyloxml string and return a TreeClass object
or a list of TreeClass object
"""
project = Phyloxml()
fo = open(saveToFile, "w+")
fo.write(xml)
fo.close()
project.build_from_file(saveToFile)
treeList = []
for tree in project.get_phylogeny():
treeList.append(TreeClass.import_from_PhyloxmlTree(tree))
if(delFile):
os.remove(saveToFile)
if len(treeList) == 1:
return treeList[0]
return treeList
def get_ete_tree(filename):
from ete3 import Tree, Phyloxml
p = Phyloxml()
p.build_from_file(filename)
t = p.get_phylogeny()[0]
return t
from ete3 import Phyloxml, phyloxml
import random
project = Phyloxml()
# Creates a random tree
phylo = phyloxml.PhyloxmlTree()
phylo.populate(5, random_branches=True)
phylo.phyloxml_phylogeny.set_name("test_tree")
# Add the tree to the phyloxml project
project.add_phylogeny(phylo)
print project.get_phylogeny()[0]
# /-iajom
# /---|
# | \-wiszh
#----|
# | /-xrygw
# \---|
# | /-gjlwx
# \---|
# \-ijvnk
# Trees can be operated as normal ETE trees
phylo.show()
# Export the project as phyloXML format
project.export()
# <phy:Phyloxml xmlns:phy="http://www.phyloxml.org/1.10/phyloxml.xsd">
# <phy:phylogeny>
from ete3 import Phyloxml
project = Phyloxml()
project.build_from_file("apaf.xml")
# Each tree contains the same methods as a PhyloTree object
for tree in project.get_phylogeny():
print tree
# you can even use rendering options
tree.show()
# PhyloXML features are stored in the phyloxml_clade attribute
for node in tree:
print "Node name:", node.name
for seq in node.phyloxml_clade.get_sequence():
for domain in seq.domain_architecture.get_domain():
domain_data = [domain.valueOf_, domain.get_from(), domain.get_to()]
print " Domain:", '\t'.join(map(str, domain_data))
from ete3 import Phyloxml, phyloxml
import random
project = Phyloxml()
# Creates a random tree
phylo = phyloxml.PhyloxmlTree()
phylo.populate(5, random_branches=True)
phylo.phyloxml_phylogeny.set_name("test_tree")
# Add the tree to the phyloxml project
project.add_phylogeny(phylo)
print project.get_phylogeny()[0]
# /-iajom
# /---|
# | \-wiszh
#----|
# | /-xrygw
# \---|
# | /-gjlwx
# \---|
# \-ijvnk
# Trees can be operated as normal ETE trees
phylo.show()
# Export the project as phyloXML format
project.export()
# <phy:Phyloxml xmlns:phy="http://www.phyloxml.org/1.10/phyloxml.xsd">
