text: import subprocess
  from master_backend import primary_pipeline, read_lexicon, parse_setup
  #This script is a wrapper around the primary pipeline script
  #which does all necessary preprocessing to generate the setup for a united states analysis.
  args = parse_setup()
  conversion = read_lexicon(args.lexicon)
  pbf = args.input
  subprocess.check_call("matUtils extract -i " + pbf + " -u samplenames.txt",shell=True)
  badsamples = open("unlabeled_samples.txt","w+")
  with open("samplenames.txt") as inf:
      with open("sample_regions.tsv","w+") as outf:
          for entry in inf:
              country = entry.split("/")[0]
              if country == "USA":
                  state = entry.split("/")[1].split("-")[0]
                  if state in conversion:
                      print(entry.strip() + "\t" + conversion[state.upper()], file = outf)
                  else:
                      print(entry.strip(), file = badsamples)
  badsamples.close()
  print("Clearing out unparseable USA samples.")
  subprocess.check_call("matUtils extract -i " + pbf + " -s unlabeled_samples.txt -p -o clean.pb", shell = True)
  #update the arguments parsed
  args.input = "clean.pb"
  args.sample_regions = "sample_regions.tsv"
  args.geojson = "us-states.geo.json"
  print("Starting main pipeline.")
  primary_pipeline(args)
  