New in version 2.1.
PhyloXML¶
PhyloXML (http://www.phyloxml.org/) is a novel standard used to encode phylogenetic information. In particular, phyloXML is designed to describe phylogenetic trees (or networks) and associated data, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events.
Loading PhyloXML projects from files¶
ETE provides full support for phyloXML projects through the
Phyloxml
object. Phylogenies are integrated as ETE’s tree
data structures as PhyloxmlTree
instances, while the rest of
features are represented as simple classes (ete2.phyloxml
)
providing basic reading and writing operations.
from ete2 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))
[Download script]
[Download example]
Each tree node contains two phyloxml elements, phyloxml_clade
and phyloxml_phylogeny
. The first attribute contains clade
information referred to the node, while phyloxml_phylogeny
contains general data about the subtree defined by each node. This
way, you can split, or copy any part of a tree and it will be exported
as a separate phyloxml phylogeny instance.
Note that node.dist
, node.support
and
node.name
features are linked to
node.phyloxml_clade.branch_length
,
node.phyloxml_clade.confidence
and
node.phyloxml_clade.name
, respectively.
Creating PhyloXML projects from scratch¶
In order to create new PhyloXML projects, a set of classes is
available in the ete2.phyloxml
module.
from ete2 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>
# <phy:name>test_tree</phy:name>
# <phy:clade>
# <phy:name>NoName</phy:name>
# <phy:branch_length>0.000000e+00</phy:branch_length>
# <phy:confidence type="branch_support">1.0</phy:confidence>
# <phy:clade>
# <phy:name>NoName</phy:name>
# <phy:branch_length>1.665083e-01</phy:branch_length>
# <phy:confidence type="branch_support">0.938507980435</phy:confidence>
# <phy:clade>
# <phy:name>NoName</phy:name>
# <phy:branch_length>1.366655e-01</phy:branch_length>
# <phy:confidence type="branch_support">0.791888248212</phy:confidence>
# <phy:clade>
# <phy:name>ojnfg</phy:name>
# <phy:branch_length>2.194209e-01</phy:branch_length>
# <phy:confidence type="branch_support">0.304705977822</phy:confidence>
# </phy:clade>
# <phy:clade>
# <phy:name>qrfnz</phy:name>
# <phy:branch_length>5.235437e-02</phy:branch_length>
# <phy:confidence type="branch_support">0.508533765418</phy:confidence>
# </phy:clade>
# </phy:clade>
# <phy:clade>
# <phy:name>shngq</phy:name>
# <phy:branch_length>9.740958e-01</phy:branch_length>
# <phy:confidence type="branch_support">0.642187390965</phy:confidence>
# </phy:clade>
# </phy:clade>
# <phy:clade>
# <phy:name>NoName</phy:name>
# <phy:branch_length>3.806412e-01</phy:branch_length>
# <phy:confidence type="branch_support">0.383619811911</phy:confidence>
# <phy:clade>
# <phy:name>vfmnk</phy:name>
# <phy:branch_length>6.495163e-01</phy:branch_length>
# <phy:confidence type="branch_support">0.141298879514</phy:confidence>
# </phy:clade>
# <phy:clade>
# <phy:name>btexi</phy:name>
# <phy:branch_length>5.704955e-01</phy:branch_length>
# <phy:confidence type="branch_support">0.951876078012</phy:confidence>
# </phy:clade>
# </phy:clade>
# </phy:clade>
# </phy:phylogeny>
# </phy:Phyloxml>