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
  import argparse
  
  
  def collect_args():
      """Returns an avian flu-specific argument parser.
      """
      parser = base.process.collect_args()
      parser.set_defaults(
          json="prepared/avian_h7n9_ha.json"
      )
      return parser
  
  
  config = {
      "dir": "avian",
      # "in": "prepared/flu_H7N9_HA.json", # should be able to specify from command line
      "geo_inference": [], # what traits to perform this on
      "auspice": { ## settings for auspice JSON export
          "panels": ['tree', 'map', 'entropy'],
          "extra_attr": [],
          "date_range": {},
          "color_options": {
              "division":{"key":"division", "legendTitle":"Division", "menuItem":"division", "type":"discrete", "color_map": []},
              "host":{"key":"host", "legendTitle":"Host", "menuItem":"host", "type":"discrete", "color_map": []},
              "num_date":{"key":"num_date", "legendTitle":"Sampling date", "menuItem":"date", "type":"continuous"},
              "gt":{"key":"genotype", "legendTitle":"Genotype", "menuItem":"genotype", "type":"discrete"}
          },
          "controls": {'geographic location':['country'], 'authors':['authors']}
      },
      "newick_tree_options": {}
  }
  
  if __name__=="__main__":
      parser = collect_args()
      params = parser.parse_args()
  
      config["in"] = params.json
      config["clean"] = params.clean
      config["newick_tree_options"]["raxml"] = not params.no_raxml
  
      runner = process(config)
      runner.align()
      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
  import argparse
  
  
  def collect_args():
      """Returns an avian flu-specific argument parser.
      """
      parser = base.process.collect_args()
      parser.set_defaults(
          json="prepared/avian_h7n9_ha.json"
      )
      return parser
  
  
  config = {
      "dir": "avian",
      # "in": "prepared/flu_H7N9_HA.json", # should be able to specify from command line
      "geo_inference": [], # what traits to perform this on
      "auspice": { ## settings for auspice JSON export
          "panels": ['tree', 'map', 'entropy'],
          "defaults": {
              "colorBy": "division",
              "geoResolution": "division"
          },
          "extra_attr": [],
          "date_range": {},
          "color_options": {
              "division":{"key":"division", "legendTitle":"Division", "menuItem":"division", "type":"discrete", "color_map": []},
              "host":{"key":"host", "legendTitle":"Host", "menuItem":"host", "type":"discrete", "color_map": []},
              "num_date":{"key":"num_date", "legendTitle":"Sampling date", "menuItem":"date", "type":"continuous"},
              "gt":{"key":"genotype", "legendTitle":"Genotype", "menuItem":"genotype", "type":"discrete"}
          },
          "controls": {'geographic location':['country'], 'authors':['authors']}
      },
      "newick_tree_options": {}
  }
  
  if __name__=="__main__":
      parser = collect_args()
      params = parser.parse_args()
  
      config["in"] = params.json
      config["clean"] = params.clean
      config["newick_tree_options"]["raxml"] = not params.no_raxml
  
      runner = process(config)
      runner.align()
      runner.build_tree()
      runner.timetree_setup_filter_run()
      #runner.run_geo_inference()
      runner.save_as_nexus()
      runner.auspice_export()
  
subject: Add colorBy and geoResolution defaults to avian