old_contents: # -*- coding: utf-8 -*-
  """anib_parser.py
  
  Provides parser for anib subcommand
  
  (c) The James Hutton Institute 2016-2019
  Author: Leighton Pritchard
  
  Contact:
  leighton.pritchard@hutton.ac.uk
  
  Leighton Pritchard,
  Information and Computing Sciences,
  James Hutton Institute,
  Errol Road,
  Invergowrie,
  Dundee,
  DD2 5DA,
  Scotland,
  UK
  
  The MIT License
  
  Copyright (c) 2016-2019 The James Hutton Institute
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in
  all copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  THE SOFTWARE.
  """
  
  from argparse import ArgumentDefaultsHelpFormatter
  
  from pyani.scripts import subcommands
  
  
  def build(subps, parents=None):
      """Return a command-line parser for the anib subcommand."""
      parser = subps.add_parser(
          "anib", parents=parents, formatter_class=ArgumentDefaultsHelpFormatter
      )
      parser.set_defaults(func=subcommands.subcmd_anib)
  
new_contents: # -*- coding: utf-8 -*-
  """anib_parser.py
  
  Provides parser for anib subcommand
  
  (c) The James Hutton Institute 2016-2019
  Author: Leighton Pritchard
  
  Contact:
  leighton.pritchard@hutton.ac.uk
  
  Leighton Pritchard,
  Information and Computing Sciences,
  James Hutton Institute,
  Errol Road,
  Invergowrie,
  Dundee,
  DD2 5DA,
  Scotland,
  UK
  
  The MIT License
  
  Copyright (c) 2016-2019 The James Hutton Institute
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in
  all copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  THE SOFTWARE.
  """
  
  from argparse import ArgumentDefaultsHelpFormatter
  
  from pyani import pyani_config
  from pyani.scripts import subcommands
  
  
  def build(subps, parents=None):
      """Return a command-line parser for the anib subcommand."""
      parser = subps.add_parser(
          "anib", parents=parents, formatter_class=ArgumentDefaultsHelpFormatter
      )
      # Required positional arguments: input and output directories
      parser.add_argument(
          action="store", dest="indir", default=None, help="input genome directory"
      )
      parser.add_argument(
          action="store",
          dest="outdir",
          default=None,
          help="output analysis results directory",
      )
      # Optional arguments
      parser.add_argument(
          "--dbpath",
          action="store",
          dest="dbpath",
          default=".pyani/pyanidb",
          help="path to pyani database",
      )
      parser.add_argument(
          "--nucmer_exe",
          dest="nucmer_exe",
          action="store",
          default=pyani_config.NUCMER_DEFAULT,
          help="path to NUCmer executable",
      )
      parser.set_defaults(func=subcommands.subcmd_anib)
  
subject: update pyani CLI parser for anib subcommand