def scale_tree_branch(tree, format="newick"):
tree_obj = None
if os.path.exists(tree):
tree_obj = Tree.get_from_path(tree, format)
elif isinstance(tree, str):
tree_obj = Tree(stream=StringIO(tree), schema=format)
elif isinstance(tree, Tree):
tree_obj = Tree
if sum([ e.length > 1 for e in tree_obj.postorder_edge_iter()]):
for e in tree_obj.postorder_edge_iter():
if e.length is not None:
e.length = e.length/100
return tree_obj.as_newick_string()
import os
##################### IMPORTANT dendropy 3.8.1 is required
if __name__ == '__main__':
taxonRemoveFile = sys.argv[1]
treeName = sys.argv[2]
outFile = sys.argv[3]
print "Prunning %s according to %s to %s" %(treeName,taxonRemoveFile ,outFile)
# tree = Tree(stream=open(treeName,"r"), schema='newick', as_rooted=True) # as_rooted=True na hole tree gulak unrooted hishabe treat korbe
#tree = TreeList.get_from_path(treeName, 'newick')
trees = dendropy.TreeList.get_from_path(treeName, 'newick',as_rooted=True,preserve_underscores=True)
# prune all taxa
handle = open(taxonRemoveFile,"r")
line = handle.readline()
taxon_sets = line.split()
handle.close()
out = open(outFile,'w');
for tree in trees:
prTree= Tree(tree)
prTree.prune_taxa_with_labels(taxon_sets, update_splits=True, delete_outdegree_one=True)
s = prTree.as_newick_string()
s = s[0:s.rfind(")")+1]
out.write(s);
out.write(";\n")
out.close()
