def parse_trees(e, otus):
"e is a nexml document parsed by etree"
from ivy.tree import Node
#from tree import Node
v = []
for tb in e.findall(NEXML + "trees"):
for te in tb.findall(NEXML + "tree"):
t = Storage()
t.attrib = Storage(te.attrib)
t.nodes = {}
for n in te.findall(NEXML + "node"):
node = Node()
if n.attrib.get("otu"):
node.isleaf = True
node.otu = otus[n.attrib["otu"]]
node.label = node.otu.label
t.nodes[n.attrib["id"]] = node
for edge in te.findall(NEXML + "edge"):
d = edge.attrib
n = t.nodes[d["target"]]
p = t.nodes[d["source"]]
length = d.get("length")
if length:
n.length = float(length)
p.add_child(n)
r = [n for n in t.nodes.values() if not n.parent]
assert len(r) == 1
r = r[0]
r.isroot = True
for i, n in enumerate(r):
n.id = i + 1
t.root = r
v.append(t)
return v
def buildtree(t, otu_id2data):
from ivy.tree import Node
if t.has_key('nodeById'):
# newer Nexson 1.2.1
node_id2data = t['nodeById']
else:
# older Nexson 1.0.0
node_id2data = {}
for n in t['node']:
node_id2data[ n['@id'] ] = n
root = None
for i, d in node_id2data.iteritems():
n = Node()
n.snode_id = i
n.taxid = None
if d.get('@root'):
n.isroot = True
root = n
oid = d.get('@otu')
if oid:
n.isleaf = True
try:
n.otu = otu_id2data[oid]
n.label = (n.otu.get('^ot:ottTaxonName') or
n.otu.get('^ot:originalLabel'))
n.taxid = n.otu.get('^ot:ottId')
except KeyError:
pass
## print t['nexson_file'], 'missing', oid
n.nexson_id = i
d['node'] = n
if t.has_key('edgeBySourceId'):
# newer Nexson 1.2.1
edges_by_source_id = t['edgeBySourceId']
else:
# older Nexson 1.0.0
edges_by_source_id = {}
for e in t['edge']:
if not edges_by_source_id.has_key( e['@source'] ):
edges_by_source_id[ e['@source'] ] = {}
edges_by_source_id[ e['@source'] ][ e['@id'] ] = e
for nid, ed in edges_by_source_id.iteritems():
n = node_id2data[nid]
for e in ed.itervalues():
cd = node_id2data[e['@target']]
c = cd['node']
c.length = e.get('@length')
n['node'].add_child(c)
root.tree_nexson = t
root.stree = t['treeid']
root.ladderize()
ivy.tree.index(root)
return root
