old_contents: #!/usr/bin/python
  
  import re
  import argparse
  import sys
  ## =================================================================
  ## Rename sequence names in fasta file so that paired end reads have different names
  ## with different suffixes: /1, or /2.
  ## =================================================================
  def RenameFasta(fastaFile, outputFile):
      '''
      '''
      g = open(outputFile,'w')
  
      with open(fastaFile, 'r') as f:
          for line in f:
              if line[0]=='>':
                  line = line.strip('\n')
                  line = line.split()
                  line = line[0] + '/' + line[1][0] + '\n'
                  g.write(line)
              else:
                  g.write(line)
  
      g.close()
  
  
  ## =================================================================
  ## argument parser
  ## =================================================================
  parser = argparse.ArgumentParser(description="Rename sequence names in fasta file so that paired end reads have different names",
                                   prog = 'RenameFasta', #program name
                                   prefix_chars='-', # prefix for options
                                   fromfile_prefix_chars='@', # if options are read from file, '@args.txt'
                                   conflict_handler='resolve', # for handling conflict options
                                   add_help=True, # include help in the options
                                   formatter_class=argparse.ArgumentDefaultsHelpFormatter # print default values for options in help message
                                   )
  
  ## input files and directories
  parser.add_argument("-i","--in",help="input fasta file",dest='fastaFile',required=True)
  
  ## output directory
  parser.add_argument("-o","--out",help="output statistics file",dest='outputFile',required=True)
  
  ## =================================================================
  ## main function
  ## =================================================================
  def main(argv=None):
      
      if argv is None:
          args = parser.parse_args()
  
      RenameFasta(args.fastaFile,args.outputFile)
  
  ##==============================================================
  ## call from command line (instead of interactively)
  ##==============================================================
  
  if __name__ == '__main__':
      sys.exit(main())
  
new_contents: #!/usr/bin/python
  
  ''' Rename sequence names in fasta file so that paired end reads have different names
      with different suffixes: /1, or /2.
  '''
  import re
  import argparse
  import sys
  ## =================================================================
  ## Rename sequence names in fasta file so that paired end reads have different names
  ## with different suffixes: /1, or /2.
  ## =================================================================
  def RenameFasta(fastaFile, outputFile):
      '''
      '''
      g = open(outputFile,'w')
  
      with open(fastaFile, 'r') as f:
          for line in f:
              if line[0]=='>':
                  line = line.strip('\n')
                  line = line.split()
                  line = line[0] + '/' + line[1][0] + '\n'
                  g.write(line)
              else:
                  g.write(line)
  
      g.close()
  
  
  ## =================================================================
  ## argument parser
  ## =================================================================
  parser = argparse.ArgumentParser(description="Rename sequence names in fasta file so that paired end reads have different names",
                                   prog = 'RenameFasta', #program name
                                   prefix_chars='-', # prefix for options
                                   fromfile_prefix_chars='@', # if options are read from file, '@args.txt'
                                   conflict_handler='resolve', # for handling conflict options
                                   add_help=True, # include help in the options
                                   formatter_class=argparse.ArgumentDefaultsHelpFormatter # print default values for options in help message
                                   )
  
  ## input files and directories
  parser.add_argument("-i","--in",help="input fasta file",dest='fastaFile',required=True)
  
  ## output directory
  parser.add_argument("-o","--out",help="output statistics file",dest='outputFile',required=True)
  
  ## =================================================================
  ## main function
  ## =================================================================
  def main(argv=None):
      
      if argv is None:
          args = parser.parse_args()
  
      RenameFasta(args.fastaFile,args.outputFile)
  
  ##==============================================================
  ## call from command line (instead of interactively)
  ##==============================================================
  
  if __name__ == '__main__':
      sys.exit(main())
  
subject: add description in the beginning