def __init__(self, edge, use_lengths=True):
children = [type(self)(child) for child in edge.Children]
TreeNode.__init__(self, Params=edge.params.copy(), Children=children,
Name=("" if children else edge.Name))
self.Length = edge.Length
self.original = edge # for edge_color_callback
self.Collapsed = False
self.use_lengths_default = use_lengths
def __init__(self, edge, use_lengths=True):
children = [type(self)(child) for child in edge.Children]
TreeNode.__init__(self, Params=edge.params.copy(), Children=children,
Name=("" if children else edge.Name))
self.Length = edge.Length
self.original = edge # for edge_color_callback
self.Collapsed = False
self.use_lengths_default = use_lengths
def make_consensus_tree(cons_split, check_for_rank=True, tips=None):
"""Returns a mapping by rank for names to their parent names and counts"""
god_node = TreeNode(Name=None)
god_node.Rank = None
base = cons_split[0]
cur_node = god_node
# create a base path in the tree
for rank, name in enumerate(base):
new_node = TreeNode(Name=name)
new_node.Rank = rank
cur_node.append(new_node)
cur_node = new_node
# setup the initial childlookup structure so taht we don't have to
# always iterate over .Children
for n in god_node.traverse(include_self=True):
if n.istip():
n.ChildLookup = {}
continue
n.ChildLookup = {n.Children[0].Name:n.Children[0]}
# for every consensus string, start at the "god" node
for idx,con in enumerate(cons_split):
cur_node = god_node
# for each name, see if we've seen it, if not, add that puppy on
for rank, name in enumerate(con):
if name in cur_node.ChildLookup:
cur_node = cur_node.ChildLookup[name]
else:
#print "adding to %s to %s" % (name, cur_node.Name)
new_node = TreeNode(Name=name)
new_node.Rank = rank
new_node.ChildLookup = {}
cur_node.append(new_node)
cur_node.ChildLookup[name] = new_node
cur_node = new_node
if tips is not None:
cur_node.append(TreeNode(Name=tips[idx]))
# build an assist lookup dict
lookup = {}
for node in god_node.traverse():
if node.Name is None:
continue
if check_for_rank and '__' in node.Name and \
node.Name.split('__')[1] == '':
continue
lookup[node.Name] = node
return god_node, lookup
def mergetree(left, right, working_dir):
"""Reconstruct a tree from merge order"""
# decorate and infer filenames for tips
global INTERNAL_COUNT
if not isinstance(left, TreeNode):
filepath = str(left[0])
name = basename(filepath.split('.')[0])
left = TreeNode(Name=name)
left.FilePath = filepath
left.Processed = False
left.PollPath = None # doesn't make sense for tips
left.FullCommand = None
left.EndTime = None
left.StartTime = None
left.TotalTime = None
if not isinstance(right, TreeNode):
filepath = str(right[0])
name = basename(filepath.split('.')[0])
right = TreeNode(Name=name)
right.FilePath = filepath
right.Processed = False
right.PollPath = None # doesn't make sense for tips
right.FullCommand = None
right.EndTime = None
right.StartTime = None
right.TotalTime = None
# internal node
name = str(INTERNAL_COUNT)
filepath = join(working_dir, name) + '.biom'
merged = TreeNode(Name=name, Children=[left, right])
merged.FilePath = filepath
merged.Processed = False
merged.PollPath = filepath + '.poll'
merged.FullCommand = None
merged.EndTime = None
merged.StartTime = None
merged.TotalTime = None
INTERNAL_COUNT += 1
return merged
def mergetree(left, right, working_dir):
"""Reconstruct a tree from merge order"""
# decorate and infer filenames for tips
global INTERNAL_COUNT
if not isinstance(left, TreeNode):
filepath = str(left[0])
name = basename(filepath.split('.')[0])
left = TreeNode(Name=name)
left.FilePath = filepath
left.Processed = False
left.PollPath = None # doesn't make sense for tips
left.FullCommand = None
left.EndTime = None
left.StartTime = None
left.TotalTime = None
if not isinstance(right, TreeNode):
filepath = str(right[0])
name = basename(filepath.split('.')[0])
right = TreeNode(Name=name)
right.FilePath = filepath
right.Processed = False
right.PollPath = None # doesn't make sense for tips
right.FullCommand = None
right.EndTime = None
right.StartTime = None
right.TotalTime = None
# internal node
name = str(INTERNAL_COUNT)
filepath = join(working_dir, name) + '.biom'
merged = TreeNode(Name=name, Children=[left, right])
merged.FilePath = filepath
merged.Processed = False
merged.PollPath = filepath + '.poll'
merged.FullCommand = None
merged.EndTime = None
merged.StartTime = None
merged.TotalTime = None
INTERNAL_COUNT += 1
return merged
