old_contents: #! /usr/bin/env python2
  #
  # This file is part of khmer, http://github.com/ged-lab/khmer/, and is
  # Copyright (C) Michigan State University, 2009-2014. It is licensed under
  # the three-clause BSD license; see doc/LICENSE.txt.
  # Contact: khmer-project@idyll.org
  #
  # pylint: disable=invalid-name,missing-docstring
  
  """
  Convert FASTQ files to FASTA format.
  
  % python scripts/fastq-to-fasta.py [ -n -o ] <fastq_name>
  
  Use '-h' for parameter help.
  """
  import sys
  import argparse
  import screed
  
  
  def get_parser():
      parser = argparse.ArgumentParser(
          description='Converts FASTQ format (.fq) files to FASTA format (.fa).',
          formatter_class=argparse.ArgumentDefaultsHelpFormatter)
  
      parser.add_argument('input_sequence', help='The name of the input'
                          ' FASTQ sequence file.')
      parser.add_argument('-o', '--output', metavar="filename",
                          help='The name of the output'
                          ' FASTA sequence file.',
                          type=argparse.FileType('w'),
                          default=sys.stdout)
      parser.add_argument('-n', '--n_keep', default=False, action='store_true',
                          help='Option to drop reads containing \'N\'s in ' +
                          'input_sequence file.')
      return parser
  
  
  def main():
      args = get_parser().parse_args()
      print >> sys.stderr, ('fastq from ', args.input_sequence)
  
      n_count = 0
      for n, record in enumerate(screed.open(args.input_sequence)):
          if n % 10000 == 0:
              print>>sys.stderr, '...', n
  
          sequence = record['sequence']
          name = record['name']
  
          if 'N' in sequence:
              if not args.n_keep:
                  n_count += 1
                  continue
  
          args.output.write('>' + name + '\n')
          args.output.write(sequence + '\n')
  
      print >> sys.stderr, '\n' + 'lines from ' + args.input_sequence
  
      if not args.n_keep:
          print >> sys.stderr, str(n_count) + ' lines dropped.'
  
      else:
          print >> sys.stderr, 'No lines dropped from file.'
  
      print >> sys.stderr, 'Wrote output to', args.output
  
  if __name__ == '__main__':
      main()
  
new_contents: #! /usr/bin/env python2
  #
  # This file is part of khmer, http://github.com/ged-lab/khmer/, and is
  # Copyright (C) Michigan State University, 2009-2014. It is licensed under
  # the three-clause BSD license; see doc/LICENSE.txt.
  # Contact: khmer-project@idyll.org
  #
  # pylint: disable=invalid-name,missing-docstring
  
  """
  Convert FASTQ files to FASTA format.
  
  % python scripts/fastq-to-fasta.py [ -n -o ] <fastq_name>
  
  Use '-h' for parameter help.
  """
  import sys
  import argparse
  import screed
  
  
  def get_parser():
      parser = argparse.ArgumentParser(
          description='Converts FASTQ format (.fq) files to FASTA format (.fa).',
          formatter_class=argparse.ArgumentDefaultsHelpFormatter)
  
      parser.add_argument('input_sequence', help='The name of the input'
                          ' FASTQ sequence file.')
      parser.add_argument('-o', '--output', metavar="filename",
                          help='The name of the output'
                          ' FASTA sequence file.',
                          type=argparse.FileType('w'),
                          default=sys.stdout)
      parser.add_argument('-n', '--n_keep', default=False, action='store_true',
                          help='Option to keep reads containing \'N\'s in ' +
                          'input_sequence file. Default is to drop reads')
      return parser
  
  
  def main():
      args = get_parser().parse_args()
      print >> sys.stderr, ('fastq from ', args.input_sequence)
  
      n_count = 0
      for n, record in enumerate(screed.open(args.input_sequence)):
          if n % 10000 == 0:
              print>>sys.stderr, '...', n
  
          sequence = record['sequence']
          name = record['name']
  
          if 'N' in sequence:
              if not args.n_keep:
                  n_count += 1
                  continue
  
          args.output.write('>' + name + '\n')
          args.output.write(sequence + '\n')
  
      print >> sys.stderr, '\n' + 'lines from ' + args.input_sequence
  
      if not args.n_keep:
          print >> sys.stderr, str(n_count) + ' lines dropped.'
  
      else:
          print >> sys.stderr, 'No lines dropped from file.'
  
      print >> sys.stderr, 'Wrote output to', args.output
  
  if __name__ == '__main__':
      main()
  
subject: Update fastq-to-fasta.py