text: #!/usr/bin/env python3
  
  import sys, os, argparse, gzip, re
  
  MY_DIR = os.path.dirname(os.path.realpath(__file__))
  PRE_DIR = os.path.join(MY_DIR, os.pardir)
  sys.path.append( PRE_DIR )
  
  import genomicFileHandler.genomic_file_handlers as genome
  
  def run():
  
      parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
  
      # Variant Call Type, i.e., snp or indel
      parser.add_argument('-infile',  '--input-file',  type=str, help='Input VCF file', required=True)
      parser.add_argument('-outfile', '--output-file', type=str, help='Output VCF file', required=True)
  
      # Parse the arguments:
      args = parser.parse_args()
      infile = args.input_file
      outfile = args.output_file
  
      return infile, outfile
  
  
  def copy(infile, outfile):
      
      with genome.open_textfile(infile) as filein, open(outfile, 'w') as fileout:
          line_i = filein.readline()
          while line_i:
              fileout.write(line_i)
              line_i = filein.readline()
  
  if __name__ == '__main__':
      infile, outfile = run()
      copy(infile, outfile)
  