old_contents: #!/usr/bin/env python
  
  """Input as a file::
  
    >ade
    GCU-U-CAUAUAAUCCUAAUGAUAUGG-UUUGGGA-GUUUCUACCAAGAG-CC--UUAAA-CUCUU---GAUUAUG-AAGU-
    (((.(.((((,,,(((((((_______.))))))).,,,,,,,,(((((((__.._____))))))...),,)))).)))).
  
  to get::
  
    >ade
    GCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGU
    ((((((((...(((((((.......)))))))........((((((.......))))))..))))))))
  
  """
  import argparse
  
  def get_parser():
      """Get parser of arguments"""
      #try:
      #parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
      #except:
      parser = argparse.ArgumentParser()#description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
      parser.add_argument('-f', '--file', help="subsection of an alignment", required=True)
      return parser
  
  def rfam_ss_notat_to_dot_bracket_notat(c):
      """Take (c)haracter and standardize ss"""
      if c in [',', '_']:
          return '.'
      if c == '<':
          return '('
      if c == '>':
          return ')'
      return c
  
  def clean_seq(seq,ss):
      #print seq, ss
      # new
      nseq = ''
      nss = ''
      for i,j in zip(seq,ss):
          if i != '-': # gap
              #print i,j
              nseq += i
              nss += rfam_ss_notat_to_dot_bracket_notat(j)
      return nseq.strip(), nss.strip()
  
  if __name__ == '__main__':
      args = get_parser().parse_args() 
  
      f = open(args.file)
      header = f.readline().strip()
      seq = f.readline()
      ss = f.readline()
      nseq, nss = clean_seq(seq,ss)
      print header
      print nseq
      print nss
  
new_contents: #!/usr/bin/env python
  
  """Input as a file::
  
    >ade
    GCU-U-CAUAUAAUCCUAAUGAUAUGG-UUUGGGA-GUUUCUACCAAGAG-CC--UUAAA-CUCUU---GAUUAUG-AAGU-
    (((.(.((((,,,(((((((_______.))))))).,,,,,,,,(((((((__.._____))))))...),,)))).)))).
  
  to get::
  
    >ade
    GCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGU
    ((((((((...(((((((.......)))))))........((((((.......))))))..))))))))
  
  """
  import argparse
  
  def get_parser():
      """Get parser of arguments"""
      #try:
      #parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
      #except:
      parser = argparse.ArgumentParser()#description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
      parser.add_argument('-f', '--file', dest="file", help="subsection of an alignment",  required=True)
      return parser
  
  def rfam_ss_notat_to_dot_bracket_notat(c):
      """Take (c)haracter and standardize ss"""
      if c in [',', '_']:
          return '.'
      if c == '<':
          return '('
      if c == '>':
          return ')'
      return c
  
  def clean_seq(seq,ss):
      #print seq, ss
      # new
      nseq = ''
      nss = ''
      for i,j in zip(seq,ss):
          if i != '-': # gap
              #print i,j
              nseq += i
              nss += rfam_ss_notat_to_dot_bracket_notat(j)
      return nseq.strip(), nss.strip()
  
  if __name__ == '__main__':
      args = get_parser().parse_args() 
  
      f = open(args.file)
      header = f.readline().strip()
      seq = f.readline()
      ss = f.readline()
      nseq, nss = clean_seq(seq,ss)
      print header
      print nseq
      print nss
  
subject: fix docs?