old_contents: from __future__ import print_function
  import os, sys
  # we assume (and assert) that this script is running from the virus directory, i.e. inside H7N9 or zika
  sys.path.append(os.path.join(os.path.dirname(__file__), '../..'))
  import base.process
  from base.process import process
  
  
  def collect_args():
      """Returns a Zika-specific argument parser.
      """
      parser = base.process.collect_args()
      parser.set_defaults(
          json="prepared/zika.json"
      )
      return parser
  
  
  config = {
      "dir": "zika",
      "in": "prepared/zika.json",
      "newick_tree_options": {"nthreads": 4},
      "clock_filter": {
          "n_iqd": 4,
      },
      "geo_inference": ['country', 'region'], # what traits to perform this on
      "geo_inference_options": {
          "root_state": {
              "region": "southeast_asia",
              "country": "vietnam",
          },
      },
      "auspice": { ## settings for auspice JSON export
          "color_options": {
              "country":{"key":"country", "legendTitle":"Country", "menuItem":"country", "type":"discrete"},
              "region":{"key":"region", "legendTitle":"Region", "menuItem":"region", "type":"discrete"},
          },
          "controls": {'authors':['authors']},
          "defaults": {'mapTriplicate': True},
          "extra_jsons": []
      },
      "timetree_options": {
          "Tc": 'opt',
          "confidence":True
      }
  }
  
  if __name__=="__main__":
      parser = collect_args()
      params = parser.parse_args()
  
      if params.clean:
          config["clean"] = True
  
      if params.json:
          config["in"] = params.json
  
      config["newick_tree_options"]["raxml"] = not params.no_raxml
  
      runner = process(config)
      runner.align(fill_gaps=True)
      runner.build_tree()
      runner.timetree_setup_filter_run()
      runner.run_geo_inference()
      runner.save_as_nexus()
      runner.auspice_export()
  
new_contents: from __future__ import print_function
  import os, sys
  # we assume (and assert) that this script is running from the virus directory, i.e. inside H7N9 or zika
  sys.path.append(os.path.join(os.path.dirname(__file__), '../..'))
  import base.process
  from base.process import process
  
  
  def collect_args():
      """Returns a Zika-specific argument parser.
      """
      parser = base.process.collect_args()
      parser.set_defaults(
          json="prepared/zika.json"
      )
      return parser
  
  
  config = {
      "dir": "zika",
      "in": "prepared/zika.json",
      "newick_tree_options": {"nthreads": 4},
      "clock_filter": {
          "n_iqd": 4,
      },
      "geo_inference": ['country', 'region'], # what traits to perform this on
      "geo_inference_options": {
          "root_state": {
              "region": "southeast_asia",
              "country": "vietnam",
          },
      },
      "auspice": { ## settings for auspice JSON export
          "color_options": {
              "country":{"key":"country", "legendTitle":"Country", "menuItem":"country", "type":"discrete"},
              "region":{"key":"region", "legendTitle":"Region", "menuItem":"region", "type":"discrete"},
          },
          "controls": {'authors':['authors']},
          "defaults": {'mapTriplicate': True}
      },
      "timetree_options": {
          "Tc": 'opt',
          "confidence":True
      }
  }
  
  if __name__=="__main__":
      parser = collect_args()
      params = parser.parse_args()
  
      if params.clean:
          config["clean"] = True
  
      if params.json:
          config["in"] = params.json
  
      config["newick_tree_options"]["raxml"] = not params.no_raxml
  
      runner = process(config)
      runner.align(fill_gaps=True)
      runner.build_tree()
      runner.timetree_setup_filter_run()
      runner.run_geo_inference()
      runner.save_as_nexus()
      runner.auspice_export()
  
subject: Fix Zika build to include all JSONs