old_contents: #! /usr/bin/env python3
  
  """Test whether given Newick/NHX trees are valid for ProPhyle.
  
  Author: Karel Brinda <kbrinda@hsph.harvard.edu>
  
  Licence: MIT
  
  Example:
  
  	$ prophyle_validate_tree.py ~/prophyle/bacteria.nw ~/prophyle/viruses.nw
  """
  
  import os
  import sys
  import argparse
  
  sys.path.append(os.path.dirname(__file__))
  import prophylelib as pro
  
  
  def main():
  	parser = argparse.ArgumentParser(description='Verify a Newick/NHX tree')
  
  	parser.add_argument('tree',
  		metavar='<tree.nw>',
  		type=str,
  		nargs='+',
  		help='phylogenetic tree (in Newick/NHX)',
  	)
  
  	args = parser.parse_args()
  	tree_fns = args.tree
  
  	ok = True
  
  	for tree_fn in tree_fns:
  		print("Validating '{}'".format(tree_fn))
  		tree = pro.load_nhx_tree(tree_fn, validate=False)
  		r = pro.validate_prophyle_nhx_tree(tree, verbose=True, throw_exceptions=False, output=sys.stdout)
  		if r:
  			print("   ...OK")
  		else:
  			ok = False
  		print()
  
  	sys.exit(0 if ok else 1)
  
  
  if __name__ == "__main__":
  	main()
  
new_contents: #! /usr/bin/env python3
  
  """Test whether given Newick/NHX trees are valid for ProPhyle.
  
  Author: Karel Brinda <kbrinda@hsph.harvard.edu>
  
  Licence: MIT
  
  Example:
  
  	$ prophyle_validate_tree.py ~/prophyle/bacteria.nw ~/prophyle/viruses.nw
  """
  
  import os
  import sys
  import argparse
  
  sys.path.append(os.path.dirname(__file__))
  import prophylelib as pro
  
  
  def main():
  	parser = argparse.ArgumentParser(description='Verify a Newick/NHX tree')
  
  	parser.add_argument('tree',
  		metavar='<tree.nw>',
  		type=str,
  		nargs='+',
  		help='phylogenetic tree (in Newick/NHX)',
  	)
  
  	args = parser.parse_args()
  	tree_fns = args.tree
  
  	ok = True
  
  	for tree_fn in tree_fns:
  		print("Validating '{}'".format(tree_fn))
  		tree = pro.load_nhx_tree(tree_fn, validate=False)
  		r = pro.validate_prophyle_nhx_tree(tree, verbose=True, throw_exceptions=False, output_fo=sys.stdout)
  		if r:
  			print("   ...OK")
  		else:
  			ok = False
  		print()
  
  	sys.exit(0 if ok else 1)
  
  
  if __name__ == "__main__":
  	main()
  
subject: Fix script for validating trees