text: #!/usr/bin/env python
  __author__ = 'Sergei F. Kliver'
  
  import argparse
  
  from Pipelines.GenomeAnnotation import RepeatAnnotation
  
  parser = argparse.ArgumentParser()
  
  parser.add_argument("-i", "--input", action="store", dest="input", required=True,
                      help="Input  fasta file with sequences")
  parser.add_argument("-f", "--path_to_trf", action="store", dest="path_to_trf", default="trf",
                      help="Path to TRF binary")
  parser.add_argument("-s", "--species", action="store", dest="species",
                      help="Species for RepeatMasker")
  parser.add_argument("-l", "--library", action="store", dest="library",
                      help="Custom repeat library for RepeatMasker")
  parser.add_argument("-d", "--output_dir", action="store", dest="output_dir", default="./",
                      help="Output directory. Default: ./")
  parser.add_argument("-p", "--output_prefix", action="store", dest="output_prefix", required=True,
                      help="Local(without /) prefix of output files")
  parser.add_argument("-t", "--threads", action="store", dest="threads", type=int,
                      help="Number of threads")
  parser.add_argument("-r", "--store_intermediate_file", action="store_true", dest="store",
                      help="Dont remove intermediate files")
  args = parser.parse_args()
  
  RepeatAnnotation.annotate_repeats(args.input, args.output_dir, args.output_prefix,
                                    repeatmasker=True, trf=True, windowmasker=True, threads=args.threads,
                                    trf_binary_path=args.path_to_trf,
                                    repeatmasker_soft_masking=True,
                                    repeatmasker_no_low_complexity=True,
                                    repeatmasker_custom_library=args.library,
                                    repeatmasker_species=args.species)
  