new_contents: """
  Convert embl format to a couple of other formats
  """
  
  import os
  import sys
  
  import argparse
  from Bio import SeqIO
  
  if __name__ == '__main__':
      parser = argparse.ArgumentParser(description="Convert EMBL format sequence files")
      parser.add_argument('-e', help='EMBL input file', required=True)
      parser.add_argument('-f', help='Store fasta file', action="store_true")
      parser.add_argument('-g', help='Store genbank file', action="store_true")
      parser.add_argument('-o', help='output file base name')
      args = parser.parse_args()
  
      outfile = args.e
      if args.o:
          outfile = args.o
  
      sin =  SeqIO.read(args.e, 'embl')
  
      if args.f:
          outfafile = outfile + ".fasta"
          sout = SeqIO.write(sin, outfafile, 'fasta')
          print("Wrote {} records to a fasta file".format(sout))
  
      if args.g:
          outgbfile = outfile + ".gbk"
          sout = SeqIO.write(sin, outgbfile, 'genbank')
          print("Wrote {} records to a genbank file".format(sout))
  
subject: convert embl to fasta or genbank