old_contents: # Copyright (c) 2015 William Lees
  
  # Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
  # documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
  # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
  # persons to whom the Software is furnished to do so, subject to the following conditions:
  
  # The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
  # Software.
  
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
  # WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
  # COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
  # OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  
  
  # List FASTA records that match the specified pattern
  
  __author__ = 'William Lees'
  __docformat__ = "restructuredtext en"
  
  import os
  import sys
  import argparse
  from Bio import SeqIO
  import re
  
  def main(argv):
      parser = argparse.ArgumentParser(description='Copy FASTA records that match the specified pattern to the output file.')
      parser.add_argument('pattern', help='pattern to match (regex')
      parser.add_argument('infile', nargs='?', type=argparse.FileType('r'), default = sys.stdin)
      parser.add_argument('outfile', nargs='?', type=argparse.FileType('w'), default = sys.stdout)
      parser.add_argument('-s', '--seq', help='copy records whose sequences match (default is to match the header)', action='store_true')
      parser.add_argument('-e', '--exc', help='copy records that do not match instead of those that do', action='store_true')
      args = parser.parse_args()
  
      if args.seq:
          pattern = re.compile(args.pattern.upper())
      else:
          pattern = re.compile(args.pattern)
  
      recs = []
      for rec in SeqIO.parse(args.infile, "fasta"):
          if args.seq:
              match = re.match(pattern, str(rec.seq).upper())
          else:
              match = re.match(pattern, rec.id)
          if (match and not args.exc) or (args.exc and not match):
              recs.append(rec)
              
      SeqIO.write(recs, args.outfile, "fasta")
              
  if __name__=="__main__":
      main(sys.argv)
  
  
new_contents: # Copyright (c) 2015 William Lees
  
  # Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
  # documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
  # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
  # persons to whom the Software is furnished to do so, subject to the following conditions:
  
  # The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
  # Software.
  
  # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
  # WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
  # COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
  # OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  
  
  # List FASTA records that match the specified pattern
  
  __author__ = 'William Lees'
  __docformat__ = "restructuredtext en"
  
  import os
  import sys
  import argparse
  from Bio import SeqIO
  import re
  
  def main(argv):
      parser = argparse.ArgumentParser(description='Copy FASTA records that match the specified pattern to the output file.')
      parser.add_argument('pattern', help='pattern to match (regex')
      parser.add_argument('infile', nargs='?', type=argparse.FileType('r'), default = sys.stdin)
      parser.add_argument('outfile', nargs='?', type=argparse.FileType('w'), default = sys.stdout)
      parser.add_argument('-s', '--seq', help='copy records whose sequences match (default is to match the header)', action='store_true')
      parser.add_argument('-e', '--exc', help='copy records that do not match instead of those that do', action='store_true')
      args = parser.parse_args()
  
      if args.seq:
          pattern = re.compile(args.pattern.upper())
      else:
          pattern = re.compile(args.pattern)
  
      recs = []
      for rec in SeqIO.parse(args.infile, "fasta"):
          if args.seq:
              match = re.match(pattern, str(rec.seq).upper())
          else:
              match = re.match(pattern, rec.description)
          if (match and not args.exc) or (args.exc and not match):
              recs.append(rec)
              
      SeqIO.write(recs, args.outfile, "fasta")
              
  if __name__=="__main__":
      main(sys.argv)
  
  
subject: Use rec.description rather than id to access full FASTA header