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
def createTreeFile(logFilname,quick,nRobots,gTime,cutDeadLeaf):
print "############################"
print "## Parsing of the logFile ##"
fileContentArray = open(options.logFile,'r').readlines()
currentTimeStamp = -1 # Detection of changement in the timestamps
precTimeStamp = -1 # Detection of changement in the timestamps
removeDone = False
beg= int(options.begin)
nGen = int(options.end)
step = int(options.step)
if(quick):table=[[-1 for i in range(nRobots)] for i in range(nGen + 1)]
allPhy = []
newAllPhy=allPhy
print "G",
for line in fileContentArray:
# A line is valid only if it starts by an interation number
#timeStampDescription = 'Info\(([0-9]+)\) : robot nb.([0-9]+) take the genome from the robot nb.([0-9]+)'
timeStampDescription = '([0-9]+) : ([0-9]+) take ([0-9]+)'
timeStampEvaluation = re.compile(timeStampDescription)
match = timeStampEvaluation.search(line)
if ( match ):
#Mechanism to detect a changement in the timestamps ( There might be many lines with the same timeStamp)
timeStamp = (int(match.group(1))+1)#/gTime
if (timeStamp > int(options.end)):
break
if ( currentTimeStamp == -1):
precTimeStamp = timeStamp
else:
precTimeStamp = currentTimeStamp
currentTimeStamp = timeStamp
newGeneration = not (precTimeStamp == currentTimeStamp)
#We continue to parse the file while we have not reached the first generation wanted
if (timeStamp >= beg) :
if(timeStamp == beg and allPhy == []) : allPhy = initAllPhy(beg-1,nRobots)
if ( newGeneration ):
print "-"+str(timeStamp),
stdout.flush()
allRoot=[]
allPhy=newAllPhy
newAllPhy = []
father = int(match.group(3))
son = int(match.group(2))
################## tree dendropy creation
sonId = str(timeStamp) + ' ' + str(son)
fatherId = str(timeStamp - 1) + ' ' + str(father)
for tree in allPhy :
if(cutDeadLeaf):
if(newGeneration):
leaves= tree.leaf_nodes()
for l in leaves:
if ( (l.level() < (timeStamp-1)) and (l.level() > 1)):
p= l.parent_node
p.remove_child(l)
while(p.is_leaf() and p.level() > 1) :
f= p.parent_node
f.remove_child(p)
p=f
n = None
ancestor = None #ancestor at the level N-S
allNodes = tree.nodes()
#Why look all node and not leaves only? Not sure but the dendropy function which gives us all leaves is faster than looking for leaves manually. And if you choose to look leaves only, be sure to no forget that they change during a generation.
for node in allNodes :
if(node.label == fatherId) :
n=node
if(n is not None):
son=n.new_child(label=sonId)
son.edge_length = 1
sonI= son.label.split(' ')[1]
gene = son.label.split(' ')[0]
if((int(timeStamp) > beg + int(step) -1) and quick ):#used to cut everythng no more useful
ancestor=son.parent_node
while( (int(getGen(son))-int(getGen(ancestor))) != int(step ) ):
ancestor = ancestor.parent_node
ancestorId = ancestor.label.split(' ')[1]
#Create a new tree using the ancestor as root
new_tree = Tree(tree)
mrca_node = new_tree.find_node_with_label(ancestor.label)
new_tree.seed_node=mrca_node
new_tree.seed_node.parent_node = None
addTree(new_tree,newAllPhy)
table[int(timeStamp)][int(sonI)]=ancestorId
else :
newAllPhy = allPhy
print "# Parsing done. #"
print "############################"
if(quick):
s=""
allFather=0
for i in table:
for j in i :
s+= str(j)+","
allFather=list(set(i))
try :
allFather.remove(-1)
except ValueError:
#if the script goes here it's because all genomes are transmitted
None
allAlive=list(i)
allAlive = filter (lambda a: a != -1, allAlive)
s+=str(len(allFather))+","+str(len(allAlive)) #The count of robots which have transmitted ther genome is bind at the end of the matrix
s+="\n"
csvFilname="./ancestorsRawData/"+baseName+".csv"
print "#\t write the csv file in "+csvFilname
out=open(csvFilname,"w" )
out.write(s)
out.close()
print "#\tdone"
print "#------------------------#"
return allPhy
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
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
