new_contents: #!/usr/bin/env python3
  #==============================================================================
  # author          : Pavel Polishchuk
  # date            : 20-08-2018
  # version         : 
  # python_version  : 
  # copyright       : Pavel Polishchuk 2018
  # license         : 
  #==============================================================================
  
  import argparse
  import os
  import re
  from subprocess import Popen
  
  
  if __name__ == '__main__':
  
      parser = argparse.ArgumentParser(description='Create fragment DB from sorted text files with context and fragments.')
      parser.add_argument('-d', '--dir', metavar='DIR', required=True,
                          help='dir where input files are stored.')
  
      args = vars(parser.parse_args())
      for o, v in args.items():
          if o == "dir": output_dir = os.path.abspath(v)
  
      job_dir = os.path.join(output_dir, 'jobs')
      if not os.path.exists(job_dir):
          os.mkdir(job_dir)
  
      pbs_name = os.path.join(job_dir, 'db_gen_%s.pbs' % (os.path.basename(output_dir)))
      script = """
      #!/usr/bin/env bash
      #PBS -l select=1:ncpus=32
      #PBS -k oe
  
      cd %s
  
      """ % output_dir
  
      for fname in sorted(os.listdir(output_dir)):
          if re.search('^r[1-5]_c\.txt$', fname):
              script += 'python3 ~/python/crem/import_env_to_db.py -i %s -o replacements.db -t radius%s -c\n' % (fname, fname[1])
  
      with open(pbs_name, "wt") as f:
          f.write(script)
      p = Popen(['qsub', pbs_name], encoding='utf8')
  
  
  
subject: Add script to run PBS jobs to collect all data to fragment database