def as_phyloxml(self, **kwargs):
"""Convert this tree to a PhyloXML-compatible Phylogeny.
This lets you use the additional annotation types PhyloXML defines, and
save this information when you write this tree as 'phyloxml'.
"""
from Bio.Phylo.PhyloXML import Phylogeny
return Phylogeny.from_tree(self, **kwargs)
def as_phyloxml(self, **kwargs):
"""Convert this tree to a PhyloXML-compatible Phylogeny.
This lets you use the additional annotation types PhyloXML defines, and
save this information when you write this tree as 'phyloxml'.
"""
from Bio.Phylo.PhyloXML import Phylogeny
return Phylogeny.from_tree(self, **kwargs)
def out():
infile = e1.get()
tree = Phylo.read(infile, "newick")
tree = Phylogeny.from_tree(tree)
tree.root.color = "#808080"
mrca = tree.common_ancestor({"name": "E"}, {"name": "F"})
mrca.color = "salmon"
tree.clade[0, 1].color = "blue"
Phylo.draw(tree)
win.destroy()
def tree_coevol(tree_folder):
"""
@tree_folder - folder name that contains all the phylogeny tree dataset
This function uses pairwise distance obtained from the tree branch lengths
to perform coevolution test.
"""
tree_data = dict()
tree_objects = glob.glob(tree_folder + "/*.*")
taxa_dict = dict()
toolbar_width = len(tree_objects)
print("Importing branch lengths\n")
for c, tree_file in enumerate(tree_objects):
tree = Phylo.read(tree_file, "newick")
phy = Phylogeny.from_tree(tree)
taxa = [x. name for x in phy.get_terminals('level')]
taxa_dict[tree_file] = (taxa)
tree_data[tree_file] = dict()
taxon_pairs = unique_pairs(taxa)
for paired_taxa in taxon_pairs:
tree_data[tree_file][paired_taxa[0] + "-" + paired_taxa[1]] = phy.distance(paired_taxa[0], paired_taxa[1])
p = str((float(c)/toolbar_width)*100)[:5]
sys.stdout.write("\r%s%%" %p)
sys.stdout.flush()
tree_pairs = unique_pairs(tree_objects)
correl = dict()
toolbar_width = len(tree_pairs)
print("Running coevolution test\n")
for c, Obj in enumerate(tree_pairs):
if len(tree_data[Obj[0]]) != len(tree_data[Obj[1]]):
common_taxa = [key for key, val in tree_data[Obj[0]].items() if key in [key2 for key2, val2 in tree_data[Obj[1]].items()]]
else:
common_taxa = tree_data[Obj[0]].keys()
correl[Obj[0].lstrip(tree_folder).lstrip("/") + "-" + Obj[1].lstrip(tree_folder).lstrip("/")] = \
pearsonr([val for key, val in _sort_dict_by_key(tree_data[Obj[0]]) if key in common_taxa], \
[val for key, val in _sort_dict_by_key(tree_data[Obj[1]]) if key in common_taxa])
p = str((float(c)/toolbar_width)*100)[:5]
sys.stdout.write("\r%s%%" %p)
sys.stdout.flush()
for key, val in correl.items():
print key, val
def phyloxml_tree_generator(tree):
children = phyloxml_tree_generator_recurse(tree, taxid=1)
return Phylogeny(name='gi2tax - Common tree', root=children)
Execução:
python bio16_filo.py
'''
#importando
from Bio import Phylo
tree = Phylo.read("simple.dnd", "newick")
print(tree)
Phylo.draw_ascii(tree)
tree.rooted = True
Phylo.draw(tree)
tree = tree.as_phyloxml()
from Bio.Phylo.PhyloXML import Phylogeny
tree = Phylogeny.from_tree(tree)
tree.root.color = (128, 128, 128)
mrca = tree.common_ancestor({"name": "E"}, {"name": "F"})
mrca.color = "salmon"
tree.clade[0, 1].color = "blue"
Phylo.draw(tree)
