def __create_taxon_set(self):
taxonset=TaxonSet()
for seq in self.aln:
taxonset.new_taxon(label=seq.id)
return taxonset
def testConflict(self):
taxa = TaxonSet([str(i) for i in xrange(1, 7)])
o = [
'(1,5,(2,((3,6),4)));',
'(2,1,(3,(6,4)));',
]
m = [o[0], o[1], '(1,5,(2,(3,6,4)));']
trees = trees_from_newick_str_list(m)
self.kernelOfTest(trees)
rng = RepeatedRandom()
for i in xrange(50):
trees = trees_from_newick_str_list(m)
for t in trees:
randomly_reorient_tree(t, rng=rng)
self.kernelOfTest(trees)
def main(argv):
# Instantiates taxon set object for tree list
taxa = TaxonSet()
# Reads in tree string from the command line
focalTree = Tree(stream=StringIO(argv[0]),
schema="newick",
rooted=False,
taxon_set=taxa)
# Iterates over all internal nodes in the focal tree (generating one constraint each)
for i in focalTree.internal_nodes():
# Defines a list that initially contains all the leaf nodes from focal tree
fullTaxonSet = focalTree.leaf_nodes()
# Iterates over all internal nodes that are not the root
if i is not focalTree.seed_node:
# Instantiates string (conTree) to hold the constraint tree string
conTree = "(("
# Iterates over leaf nodes that are descendants of the current internal node
for j in i.leaf_nodes():
# Appropriately adds the taxon name to the constraint tree string
if j is i.leaf_nodes()[0]:
conTree = conTree + str(j.taxon)
else:
conTree = conTree + "," + str(j.taxon)
# Closes out the part of the constraint for taxa descended from the focal node
conTree = conTree + ")"
# Takes all leaves and removes those descended from the focal node
for j in i.leaf_nodes():
fullTaxonSet.remove(j)
# Adds all leaves not descended from the focal node to the constraint tree string
for j in fullTaxonSet:
conTree = conTree + "," + str(j.taxon)
# Closes constraint tree string
conTree = conTree + ")"
# Prints constraint tree string to the screen
print conTree
def rdf2dendropyTree(file_obj=None, data=None):
'''
Parses the content (a `file_obj` file object or `data` as a) into a dendropyTree.
Uses the 'has_Parent' term in http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#
to construct and return a rooted dendropy.Tree object
Relies on rdflib and dendropy.
Raises ValueError if the graph does not imply exactly 1 root node
'''
from dendropy import Node, Tree, Edge, TaxonSet, Taxon
graph = rdflib.Graph()
if file_obj:
graph.parse(file=file_obj)
else:
graph.parse(data=data, format='xml')
nd_dict = {}
has_parent_predicate = OBO_PREFIX + HAS_PARENT_PREDICATE
if _DEBUGGING:
out = open('parse_rdf.txt', 'w')
taxon_set = TaxonSet()
OBO = rdflib.Namespace(u"http://purl.obolibrary.org/obo/")
parentless = set()
for s, p, o in graph.triples((None, OBO[HAS_PARENT_PREDICATE], None)):
parent = nd_dict.get(id(o))
if parent is None:
#print 'Parent o.value = ', o.value(rdflib.RDF.nodeID)
raw_o = o
o = rdflib.resource.Resource(graph, o)
o_tu = o.value(OBO[REPRESENTS_TU_PREDICATE])
if o_tu:
o_label = o_tu.value(rdflib.RDFS.label)
t = Taxon(label=o_label)
taxon_set.append(t)
parent = Node(taxon=t)
else:
parent = Node()
nd_dict[id(raw_o)] = parent
parentless.add(parent)
child = nd_dict.get(id(s))
if child is None:
raw_s = s
s = rdflib.resource.Resource(graph, s)
s_tu = s.value(OBO[REPRESENTS_TU_PREDICATE])
if s_tu:
s_label = s_tu.value(rdflib.RDFS.label)
t = Taxon(label=s_label)
taxon_set.append(t)
child = Node(taxon=t)
else:
child = Node()
nd_dict[id(raw_s)] = child
else:
if child in parentless:
parentless.remove(child)
parent.add_child(child)
if _DEBUGGING:
out.write('%s %s %s\n' % ( str(s), p, o))
out.write('%s\n' % ( str(parentless)))
if _DEBUGGING:
out.close()
if len(parentless) != 1:
message = "Expecting to find exactly Node (an object of a has_Parent triple) in the graph without a parent. Found %d" % len(parentless)
CUTOFF_FOR_LISTING_PARENTLESS_NODES = 1 + len(parentless) # we might want to put in a magic number here to suppress really long output
if len(parentless) > 0 and len(parentless) < CUTOFF_FOR_LISTING_PARENTLESS_NODES:
message += ":\n "
for i in parentless:
if i.label:
message += "\n " + i.label
else:
message += "\n <unlabeled>" + str(id(i))
raise ValueError(message)
else:
return None
tree = Tree(taxon_set=taxon_set)
tree.seed_node = list(parentless)[0]
tree.is_rooted = True
return tree
'--schema',
dest='schema',
type='str',
default="newick",
help='The format/schema of the input data')
parser.add_option('-g',
'--gordon',
dest='gordons',
action="store_true",
default=False,
help="Specify to use the Gordon's strict consensus")
(options, args) = parser.parse_args()
if len(args) == 0:
sys.exit("Expecting a filename as an argument")
schema = options.schema.upper()
trees = []
taxon_set = TaxonSet()
dataset = DataSet(taxon_set=taxon_set)
if schema == "PHYLIP":
schema = "NEWICK"
for f in args:
fo = open(f, "rU")
dataset.read(stream=fo, schema=schema)
for tl in dataset.tree_lists:
trees.extend(tl)
o = inplace_strict_consensus_merge(trees,
gordons_supertree=options.gordons)
sys.stdout.write("%s;\n" % str(o))
def rdf2dendropyTree(file_obj=None, data=None):
'''
Parses the content (a `file_obj` file object or `data` as a) into a dendropyTree.
Uses the 'has_Parent' term in http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#
to construct and return a rooted dendropy.Tree object
Relies on rdflib and dendropy.
Raises ValueError if the graph does not imply exactly 1 root node
'''
from dendropy import Node, Tree, Edge, TaxonSet, Taxon
graph = rdflib.Graph()
if file_obj:
graph.parse(file=file_obj)
else:
graph.parse(data=data, format='xml')
nd_dict = {}
has_parent_predicate = OBO_PREFIX + HAS_PARENT_PREDICATE
if _DEBUGGING:
out = open('parse_rdf.txt', 'w')
taxon_set = TaxonSet()
OBO = rdflib.Namespace(u"http://purl.obolibrary.org/obo/")
parentless = set()
for s, p, o in graph.triples((None, OBO[HAS_PARENT_PREDICATE], None)):
parent = nd_dict.get(id(o))
if parent is None:
#print 'Parent o.value = ', o.value(rdflib.RDF.nodeID)
raw_o = o
o = rdflib.resource.Resource(graph, o)
o_tu = o.value(OBO[REPRESENTS_TU_PREDICATE])
if o_tu:
o_label = o_tu.value(rdflib.RDFS.label)
t = Taxon(label=o_label)
taxon_set.append(t)
parent = Node(taxon=t)
else:
parent = Node()
nd_dict[id(raw_o)] = parent
parentless.add(parent)
child = nd_dict.get(id(s))
if child is None:
raw_s = s
s = rdflib.resource.Resource(graph, s)
s_tu = s.value(OBO[REPRESENTS_TU_PREDICATE])
if s_tu:
s_label = s_tu.value(rdflib.RDFS.label)
t = Taxon(label=s_label)
taxon_set.append(t)
child = Node(taxon=t)
else:
child = Node()
nd_dict[id(raw_s)] = child
else:
if child in parentless:
parentless.remove(child)
parent.add_child(child)
if _DEBUGGING:
out.write('%s %s %s\n' % (str(s), p, o))
out.write('%s\n' % (str(parentless)))
if _DEBUGGING:
out.close()
if len(parentless) != 1:
message = "Expecting to find exactly Node (an object of a has_Parent triple) in the graph without a parent. Found %d" % len(
parentless)
CUTOFF_FOR_LISTING_PARENTLESS_NODES = 1 + len(
parentless
) # we might want to put in a magic number here to suppress really long output
if len(parentless) > 0 and len(
parentless) < CUTOFF_FOR_LISTING_PARENTLESS_NODES:
message += ":\n "
for i in parentless:
if i.label:
message += "\n " + i.label
else:
message += "\n <unlabeled>" + str(id(i))
raise ValueError(message)
else:
return None
tree = Tree(taxon_set=taxon_set)
tree.seed_node = list(parentless)[0]
tree.is_rooted = True
return tree
import os
import pandas as pd
o_file = sys.argv[2]
i_file = sys.argv[1]
ilist = find_files(top=i_file, filename_filter='RAxML_bipartitions.*')
olist = find_files(top=o_file, filename_filter='RAxML_bipartitions.*')
split1 = [os.path.split(file)[1][19:] for file in ilist]
split2 = [os.path.split(file)[1][19:-4] for file in olist]
part_bss = []
unpart_bss = []
SD = []
bs1 = []
tree3 = []
tree2 = []
shared_files = []
t = TaxonSet()
for file in split1:
if file in split2:
print file
tree1 = dendropy.Tree.get_from_path('%sRAxML_bipartitions.%s.phy' %
(o_file, file),
'newick',
taxon_set=t)
tree3.append(tree1)
print tree1
tree1 = dendropy.Tree.get_from_path('%sRAxML_bipartitions.%s' %
(i_file, file),
'newick',
taxon_set=t)
tree2.append(tree1)
print tree1
def rdf2dendropyTree(filepath):
from rdflib.graph import Graph
from dendropy import Node, Tree, Edge, TaxonSet, Taxon
graph = Graph()
graph.parse(filepath)
nd_dict = {}
has_parent_predicate = OBO_PREFIX + HAS_PARENT_PREDICATE
if _DEBUGGING:
out = open("parse_rdf.txt", "w")
taxon_set = TaxonSet()
OBO = Namespace(u"http://purl.obolibrary.org/obo/")
parentless = set()
for s, p, o in graph.triples((None, OBO[HAS_PARENT_PREDICATE], None)):
parent = nd_dict.get(id(o))
if parent is None:
# print 'Parent o.value = ', o.value(rdflib.RDF.nodeID)
raw_o = o
o = rdflib.resource.Resource(graph, o)
o_tu = o.value(OBO[REPRESENTS_TU_PREDICATE])
if o_tu:
o_label = o_tu.value(rdflib.RDFS.label)
t = Taxon(label=o_label)
taxon_set.append(t)
parent = Node(taxon=t)
else:
parent = Node()
nd_dict[id(raw_o)] = parent
parentless.add(parent)
child = nd_dict.get(id(s))
if child is None:
raw_s = s
s = rdflib.resource.Resource(graph, s)
s_tu = s.value(OBO[REPRESENTS_TU_PREDICATE])
if s_tu:
s_label = s_tu.value(rdflib.RDFS.label)
t = Taxon(label=s_label)
taxon_set.append(t)
child = Node(taxon=t)
else:
child = Node()
nd_dict[id(raw_s)] = child
else:
if child in parentless:
parentless.remove(child)
parent.add_child(child)
if _DEBUGGING:
out.write("%s %s %s\n" % (str(s), p, o))
out.write("%s\n" % (str(parentless)))
if _DEBUGGING:
out.close()
if len(parentless) != 1:
message = (
"Expecting to find exactly Node (an object of a has_Parent triple) in the graph without a parent. Found %d"
% len(parentless)
)
CUTOFF_FOR_LISTING_PARENTLESS_NODES = 1 + len(
parentless
) # we might want to put in a magic number here to suppress really long output
if len(parentless) > 0 and len(parentless) < CUTOFF_FOR_LISTING_PARENTLESS_NODES:
message += ":\n "
for i in parentless:
if i.label:
message += "\n " + i.label
else:
message += "\n <unlabeled>" + str(id(i))
raise ValueError(message)
else:
sys.exit("no parentless")
return None
tree = Tree(taxon_set=taxon_set)
tree.seed_node = list(parentless)[0]
tree.is_rooted = True
return tree
def trees_from_newick_str_list(newick_list):
all_tree_str = " ".join(newick_list)
return TreeList(stream=StringIO(all_tree_str),
taxon_set=TaxonSet(),
schema="NEWICK")
default=4,
help='The number of leaves to generate.')
parser.add_option('-s',
'--seed',
action='store',
dest='seed',
type=long,
default=0,
help='The seed of the random number generator')
(opts, args) = parser.parse_args()
num_leaves = opts.num_leaves
if num_leaves < 3:
sys.exit("The number of leaves must be greater than 2")
seed = opts.seed
if seed < 0:
sys.exit("Seed must be positive")
if seed < 1:
seed = time.time()
rng = random.Random()
sys.stderr.write("seed = %ld\n" % seed)
rng.seed(seed)
outstr = sys.stdout
taxa = TaxonSet(["t%d" % i for i in xrange(1, 1 + num_leaves)])
tree = uniform_pure_birth(taxa, rng=rng)
for e in tree.preorder_edge_iter():
e.length = rng.random()
outstr.write("%s;\n" % tree.as_newick_string(preserve_spaces=True))