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.
  """
  
  from Bio import SeqIO
  
  from rnacentral_pipeline.writers import build_entry_writer
  
  from . import helpers
  
  
  def parse(handle):
      """
      Parse all entries in the handle to produce an iterable of all RefSeq
      entries.
      """
  
      for record in SeqIO.parse(handle, "genbank"):
          source = record.features[0]
          assert source.type == 'source'
          for ncrna in helpers.ncrna_features(record.features[1:]):
              yield helpers.as_entry(record, source, ncrna)
  
  
  def from_file(handle, output):
      writer = build_entry_writer(parse)
      writer(output, handle)
  
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.
  """
  
  from Bio import SeqIO
  
  from . import helpers
  
  
  def parse(handle):
      """
      Parse all entries in the handle to produce an iterable of all RefSeq
      entries.
      """
  
      for record in SeqIO.parse(handle, "genbank"):
          source = record.features[0]
          assert source.type == 'source'
          for ncrna in helpers.ncrna_features(record.features[1:]):
              yield helpers.as_entry(record, source, ncrna)
  
subject: Remove unneeded function