old_contents: #!/usr/bin/env python
  
  from dark.summarize import summarizeReads
  import sys
  
  
  if len(sys.argv) != 2:
      print('Usage: %s file.fasta / file.fastq' % sys.argv[0], file=sys.stderr)
      sys.exit(1)
  else:
      filename = sys.argv[1]
      if filename.lower().endswith('q'):
          filetype = 'fastq'
      else:
          # Assume anything not ending with a 'q' is fasta.
          filetype = 'fasta'
  
      result = summarizeReads(filename, filetype)
  
      print('Number of reads:', result['read_number'])
      print('Total length: %s bases' % result['total_length'])
      print('The average read length: %s bases' % result['average_length'])
      print('Longest read:', result['max_length'])
      print('Shortest read:', result['min_length'])
      print('Median length:', result['median_length'])
  
      for base, count in result['base_counts'].items():
          print('%s: Total: %s; Average per read: %s' % (
              base, count, count / result['read_number']))
  
new_contents: #!/usr/bin/env python
  
  from dark.summarize import summarizeReads
  import sys
  
  
  if len(sys.argv) != 2:
      print('Usage: %s file.fasta / file.fastq' % sys.argv[0], file=sys.stderr)
      sys.exit(1)
  else:
      filename = sys.argv[1]
      if filename.lower().endswith('q'):
          filetype = 'fastq'
      else:
          # Assume anything not ending with a 'q' is fasta.
          filetype = 'fasta'
  
      result = summarizeReads(filename, filetype)
  
      print('Number of reads:', result['read_number'])
      print('Total length: %s bases' % result['total_length'])
      print('The average read length: %s bases' % result['average_length'])
      print('Longest read:', result['max_length'])
      print('Shortest read:', result['min_length'])
      print('Median length:', result['median_length'])
  
      for base in sorted(result['base_counts']):
          count = result['base_counts'][base]
          print('%s: Total: %s; Average per read: %s' % (
              base, count, count / result['read_number']))
  
subject: print bases in a sorted order in summarize-reads.py