def exclude_tip(tip, tree, verbose=False):
"""Return pruned tree with tip excluded
tip -- a PyCogent PhyloNode object from the tree
tree -- a PyCogent PhyloNode object (the tree)
NOTE: This function exists to support distance-based exclusion of
neightbors. For holdout analysis we really want to
exclude the organism in the trait table rather than the tree.
"""
# Make sure the tip is really a tip
if not tip.isTip():
raise ValueError(
"The 'holdout' fn got a non-tip node for it's 'tip' parameter.")
#Old exclusion based method...but for large trees this is quite slow
# Assuming that's OK, remove the tip
#if tip.Parent is not None:
# removal_ok = tip.Parent.remove(tip)
#else:
# removal_ok = False
#if not removal_ok:
# raise ValueError("holdout could not remove node '%s' from tree." %(tip.Name))
#tree.prune()
#Newer subtree based method
tips_to_keep = [t.Name for t in tree.tips() if t.Name != tip.Name]
if verbose:
print "Generating subtree with %i tips" % len(tips_to_keep)
subtree = get_sub_tree(tree, tips_to_keep)
return subtree
def exclude_tip(tip, tree,verbose=False):
"""Return pruned tree with tip excluded
tip -- a PyCogent PhyloNode object from the tree
tree -- a PyCogent PhyloNode object (the tree)
NOTE: This function exists to support distance-based exclusion of
neightbors. For holdout analysis we really want to
exclude the organism in the trait table rather than the tree.
"""
# Make sure the tip is really a tip
if not tip.isTip():
raise ValueError("The 'holdout' fn got a non-tip node for it's 'tip' parameter.")
#Old exclusion based method...but for large trees this is quite slow
# Assuming that's OK, remove the tip
#if tip.Parent is not None:
# removal_ok = tip.Parent.remove(tip)
#else:
# removal_ok = False
#if not removal_ok:
# raise ValueError("holdout could not remove node '%s' from tree." %(tip.Name))
#tree.prune()
#Newer subtree based method
tips_to_keep = [t.Name for t in tree.tips() if t.Name != tip.Name]
if verbose:
print "Generating subtree with %i tips" %len(tips_to_keep)
subtree = get_sub_tree(tree,tips_to_keep)
return subtree
def exclude_tip_neighbors(tip,tree, verbose=False):
# check that the exclusion distance won't exclude the entire tree
max_dist = tree.maxTipTipDistance()[0]
tips_to_delete = tip.tipsWithinDistance(exclusion_distance)
tips_to_delete = [t.Name for t in tips_to_delete]
if verbose:
print "Tips to delete:",len(tips_to_delete)
tips_to_keep = [t.Name for t in tree.tips() if t.Name not in tips_to_delete]
if float(exclusion_distance) > float(max_dist) or \
len(tips_to_delete) == len(tree.tips()):
raise ValueError("specified tree would be entirely excluded because branch lengths are too short")
#holdout_tip = tip
holdout_tip = tip.Name
#We're working with the *pruned* tree so we want the holdout tip
#removed
if holdout_tip in tips_to_keep:
tips_to_keep.remove(holdout_tip)
if verbose:
print "Will remove our tip of interest from the tree: {0}".format(holdout_tip)
if verbose:
print "Tips to keep:", len(tips_to_keep)
subtree = get_sub_tree(tree,tips_to_keep)
del tree
# Then it's neighbors
#for tip in tips_to_delete:
# if tip == holdout_tip:
# #Don't exclude the tip you're testing
# continue
# tree = exclude_tip(tip,tree)
return subtree
def exclude_tip_neighbors(tip,tree, verbose=False):
# check that the exclusion distance won't exclude the entire tree
max_dist = tree.maxTipTipDistance()[0]
tips_to_delete = tip.tipsWithinDistance(exclusion_distance)
tips_to_delete = [t.Name for t in tips_to_delete]
if verbose:
print "Tips to delete:",len(tips_to_delete)
tips_to_keep = [t.Name for t in tree.tips() if t.Name not in tips_to_delete]
if float(exclusion_distance) > float(max_dist) or \
len(tips_to_delete) == len(tree.tips()):
raise ValueError("specified tree would be entirely excluded because branch lengths are too short")
#holdout_tip = tip
holdout_tip = tip.Name
#We're working with the *pruned* tree so we want the holdout tip
#removed
if holdout_tip in tips_to_keep:
tips_to_keep.remove(holdout_tip)
if verbose:
print "Will remove our tip of interest from the tree: {0}".format(holdout_tip)
if verbose:
print "Tips to keep:", len(tips_to_keep)
subtree = get_sub_tree(tree,tips_to_keep)
del tree
# Then it's neighbors
#for tip in tips_to_delete:
# if tip == holdout_tip:
# #Don't exclude the tip you're testing
# continue
# tree = exclude_tip(tip,tree)
return subtree