old_contents: """
  This file can be downloaded and used to create a .txt file containing only
  the accession numbers from the ghost-tree.nwk that you plan to use for your
  analyses.
  
  You must have skbio installed. http://scikit-bio.org/
  
  You will then use "ghost_tree_tips.txt" output file containing the accession
  numbers to filter your .biom table so that it contains only the OTUs that
  are in the ghost-tree.nwk that you are using.
  
  http://qiime.org/scripts/filter_otus_from_otu_table.html
  
  Use the required arguments and the following two optional arguments:
  -e, --otu_ids_to_exclude_fp
  (provide the text file containing OTU ids to exclude)
  --negate_ids_to_exclude
  (this will keep OTUs in otu_ids_to_exclude_fp, rather than discard them)
  """
  from skbio import TreeNode
  
  ghosttree = TreeNode.read("ghost_tree_97_80clusters_from_alpha_release.nwk")  # insert your ghost-tree name here
  output = open("ghost_tree_tips.txt", "w")
  
  for node in ghosttree.tips():
      output.write(str(node.name)+"\n")
  
  output.close()
  
new_contents: """
  This file can be downloaded and used to create a .txt file containing only
  the accession numbers from the ghost-tree.nwk that you plan to use for your
  analyses.
  
  You must have skbio installed. http://scikit-bio.org/
  If you aren't familiar with skbio, make sure to check it out on its own, too!
  
  You will then use "ghost_tree_tips.txt" output file containing the accession
  numbers to filter your .biom table so that it contains only the OTUs that
  are in the ghost-tree.nwk that you are using.
  
  http://qiime.org/scripts/filter_otus_from_otu_table.html
  
  Use the required arguments and the following two optional arguments:
  -e, --otu_ids_to_exclude_fp
  (provide the text file containing OTU ids to exclude)
  --negate_ids_to_exclude
  (this will keep OTUs in otu_ids_to_exclude_fp, rather than discard them)
  """
  from skbio import TreeNode
  
  ghosttree = TreeNode.read("ghost_tree_97_80clusters_from_alpha_release.nwk",
                            convert_underscores=False)  # your file goes here
  output = open("ghost_tree_tips_underscore_fix.txt", "w")
  
  for node in ghosttree.tips():
      output.write(str(node.name)+"\n")
  
  output.close()
  
subject: fix #56 fix #67 underscore preservation