old_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2017] EMBL-European Bioinformatics Institute
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at
  http://www.apache.org/licenses/LICENSE-2.0
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
  """
  
  import re
  import itertools as it
  
  from Bio import SeqIO
  
  NHMMER_PATTERN = re.compile('^[ABCDGHKMNRSTVWXYU]+$', re.IGNORECASE)
  
  
  def is_valid_nhmmer_record(record):
      """
      Checks if a sequence is valid for nhmmer usage.
      """
      return bool(NHMMER_PATTERN.match(str(record.seq)))
  
  
  def valid_nhmmer(handle, output):
      sequences = SeqIO.parse(handle, 'fasta')
      accepted = filter(is_valid_nhmmer_record, sequences)
      SeqIO.write(accepted, output, 'fasta')
  
  
  def invalid_nhmmer(handle, output):
      sequences = SeqIO.parse(handle, 'fasta')
      rejected = filterfalse(is_valid_nhmmer_record, sequences)
      SeqIO.write(rejected, output, 'fasta')
  
new_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2017] EMBL-European Bioinformatics Institute
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at
  http://www.apache.org/licenses/LICENSE-2.0
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
  """
  
  import re
  import itertools as it
  
  from Bio import SeqIO
  
  NHMMER_PATTERN = re.compile('^[ABCDGHKMNRSTVWXYU]+$', re.IGNORECASE)
  
  
  def is_valid_nhmmer_record(record):
      """
      Checks if a sequence is valid for nhmmer usage.
      """
      return bool(NHMMER_PATTERN.match(str(record.seq)))
  
  
  def valid_nhmmer(handle, output):
      sequences = SeqIO.parse(handle, 'fasta')
      accepted = filter(is_valid_nhmmer_record, sequences)
      SeqIO.write(accepted, output, 'fasta')
  
  
  def invalid_nhmmer(handle, output):
      sequences = SeqIO.parse(handle, 'fasta')
      rejected = it.filterfalse(is_valid_nhmmer_record, sequences)
      SeqIO.write(rejected, output, 'fasta')
  
subject: Correct function call