old_contents: from __future__ import print_function
  import os, sys
  sys.path.append('..') # we assume (and assert) that this script is running from the virus directory, i.e. inside H7N9 or zika
  from base.process import process
  import argparse
  
  parser = argparse.ArgumentParser(description = "Process a prepared zika JSON")
  parser.add_argument('--clean', action='store_true', help="clean build (remove previous checkpoints)")
  
  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,
      },
      "newick_tree_options":{
          "raxml": True
      }
  }
  
  if __name__=="__main__":
      params = parser.parse_args()
      if params.clean: config["clean"] = True
      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
  sys.path.append('..') # we assume (and assert) that this script is running from the virus directory, i.e. inside H7N9 or zika
  from base.process import process
  import argparse
  
  parser = argparse.ArgumentParser(description = "Process a prepared zika JSON")
  parser.add_argument('--clean', action='store_true', help="clean build (remove previous checkpoints)")
  
  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,
      },
      "newick_tree_options":{
          "raxml": True
      }
  }
  
  if __name__=="__main__":
      params = parser.parse_args()
      if params.clean: config["clean"] = True
      runner = process(config)
      runner.align(fill_gaps=True)
      runner.build_tree()
      runner.timetree_setup_filter_run()
      runner.run_geo_inference()
      runner.auspice_export()
  
subject: remove zika's "save as nexus" functionality - this is now a script