def main(): treefile1 = sys.argv[1] treefile2 = sys.argv[2] treelist = TreeList() treelist.read(file=open(treefile1, 'rU'), schema="nexus") treelist.read(file=open(treefile2, 'rU'), schema="nexus") if treecompare.symmetric_difference(treelist.__getitem__(0), treelist.__getitem__(1)) == 0: print "trees are identical" else: print "trees are NOT identical"
def readTree(filename, quiet=False): if not quiet: print() print("Reading in files...") print() temp = TreeList() try: temp.read(file=open(filename, 'r'), schema="newick", preserve_underscores=True) except: print("Error with file '{}': please only use files with newick tree format".format(f)) sys.exit() return temp
def readTrees(filenames, namespace, quiet=False): if not quiet: print() print("Reading in files...") print() sample_tree_list = [] for f in filenames: # temp = TreeList(taxon_namespace=namespace) temp = TreeList() try: temp.read(file=open(f, 'r'), schema="newick", preserve_underscores=True) except: print( "Error with file '{}': please only use files with newick tree format" .format(f)) sys.exit() sample_tree_list.append(temp) return sample_tree_list
#! /usr/bin/env python from dendropy import TreeList from sys import argv trees = TreeList() trees.read(path=argv[1],schema="newick") trees.write(path=argv[2],schema="nexus")