new_contents: #Gemini wrapper
  import argparse
  from subprocess import run
  from pynnotator import settings
  import os
  
  class GnomAD:
      def __init__(self, vcf, cores):
          self.data = []
  
      def install():
          print('Install gnomAD')
  
          os.chdir(settings.data_dir)
  
          
          if not os.path.exists('gnomad'):
              os.makedirs('gnomad')
          os.chdir('gnomad')
  
          filepath = 'gnomad.genomes.r2.1.sites.vcf.bgz'
          if not os.path.isfile(filepath):
              command = 'wget -c https://storage.googleapis.com/gnomad-public/release/2.1/vcf/genomes/{}'.format(filepath)
              run(command, shell=True)
          filepath = 'gnomad.genomes.r2.1.sites.vcf.bgz.tbi'
          if not os.path.isfile(filepath):
              command = 'wget -c https://storage.googleapis.com/gnomad-public/release/2.1/vcf/genomes/{}'.format(filepath)
              run(command, shell=True)
          
          filepath = 'gnomad.exomes.r2.1.sites.vcf.bgz'
          if not os.path.isfile(filepath):
              command = 'wget -c https://storage.googleapis.com/gnomad-public/release/2.1/vcf/exomes/{}'.format(filepath)
              run(command, shell=True)
          filepath = 'gnomad.exomes.r2.1.sites.vcf.bgz.tbi'
          if not os.path.isfile(filepath):
              command = 'wget -c https://storage.googleapis.com/gnomad-public/release/2.1/vcf/exomes/{}'.format(filepath)
              run(command, shell=True)
  
      def main(self):
          #command = '
          print('Annotate GnomAD')
          command = ''
  
  
  
  if __name__ == '__main__':
      
      parser = argparse.ArgumentParser(description='Annotate a VCF File with GnomAD.')
  
      parser.add_argument('options', help='install test', nargs='?')
      parser.add_argument('-i', dest='vcf_file', required=False, metavar='example.vcf', help='a VCF file to be annotated')
      parser.add_argument('-n', dest='cores', required=False, metavar='4', help='number of cores to use')
  
      args = parser.parse_args()
      gnomead = GnomAD(args.vcf_file, args.cores)
      if args.options == 'install':
          gnomead.install()
      else:
          gnomead.main()
  
subject: add gnomad