text: # Dan Blankenberg
  from __future__ import print_function
  
  import sys
  
  
  def main():
      input_filename = sys.argv[1]
      output_filename = sys.argv[2]
      identifier_col = int(sys.argv[3]) - 1
      sequence_col = int(sys.argv[4]) - 1
      quality_col = int(sys.argv[5]) - 1
  
      max_col = max(identifier_col, sequence_col, quality_col)
      num_reads = None
      skipped_lines = 0
      with open(output_filename, 'w') as out:
          for num_reads, line in enumerate(open(input_filename)):
              fields = line.rstrip('\n\r').split('\t')
              if len(fields) > max_col:
                  out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col]))
              else:
                  skipped_lines += 1
  
      if num_reads is None:
          print("Input was empty.")
      else:
          print("%i tabular lines were written as FASTQ reads. Be sure to use the FASTQ Groomer tool on this output before further analysis." % (num_reads + 1 - skipped_lines))
  
  
  if __name__ == "__main__":
      main()
  