def get_subtree(self, taxa):
if len(taxa) == 0:
return None
tree = Tree(self._tree)
if isinstance(taxa[0],str):
tree.prune_taxa_with_labels(taxa)
elif isinstance(taxa[0],Taxon):
tree.prune_taxa(taxa)
return PhylogeneticTree(tree)
def get_subtree(self, taxa):
if len(taxa) == 0:
return None
tree = Tree(self._tree)
if isinstance(taxa[0], str):
tree.prune_taxa_with_labels(taxa)
elif isinstance(taxa[0], Taxon):
tree.prune_taxa(taxa)
return PhylogeneticTree(tree)
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()
