new_contents: """
  this scripts takes the enigma variant list and do various things with it, inlcuding:
      1. convert HGVS to genomic coordinate
  """
  
  import hgvs.dataproviders.uta
  import hgvs.parser
  import hgvs.variantmapper
  import pyhgvs
  
  
  
  def main():
      enigma_file = open("data/Enigma_variants/enigma-database.tsv", "r")
      line_num = 0
      for line in enigma_file:
          line_num += 1
          if line_num == 1:
              pass 
          else:
              items = line.strip().split("\t")
              transcript_id = items[1]
              HGVS = items[2]
              hgvs_c = transcript_id + ":" + HGVS
              genome = convert_hgvs_to_genome(hgvs_c)
              items.append(genome)
  
  def convert_hgvs_to_genome(hgvs_c):
      hp = hgvs.parser.Parser()
      print hgvs_c
      hgvs_c = hp.parse_hgvs_variant(hgvs_c)
      hdp = hgvs.dataproviders.uta.connect()
      evm = hgvs.variantmapper.EasyVariantMapper(hdp,
          primary_assembly='GRCh37', alt_aln_method='splign')
      hgvs_g = evm.c_to_g(hgvs_c)
      hgvs_p = evm.c_to_p(hgvs_c)
      hgvs_n = evm.c_to_n(hgvs_c)
      print hgvs_n
      print " "
  
  
  
  
  
  if __name__ == "__main__":
      main()
  
subject: add code to process enigma variants