old_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2018] 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 os
  import re
  
  from pathlib import Path
  
  import typing as ty
  
  import attr
  from attr.validators import instance_of as is_a
  
  from rnacentral_pipeline import ribovore
  from rnacentral_pipeline.databases.data import RibovoreResult
  
  
  def as_dict(directory: Path, allow_missing=False) -> ty.Dict[str, RibovoreResult]:
      try:
          results = ribovore.parse_directory(path)
          return {p.target: p for p in results if p.status != 'FAIL'}
      except ValueError as e:
          if not allow_missing:
              raise ValueError("No ribovore result file in: %s " % directory)
          return {}
  
new_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2018] 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 os
  import re
  
  from pathlib import Path
  
  import typing as ty
  
  import attr
  from attr.validators import instance_of as is_a
  
  from rnacentral_pipeline import ribovore
  from rnacentral_pipeline.databases.data import RibovoreResult
  
  
  def as_dict(directory: Path, allow_missing=False) -> ty.Dict[str, RibovoreResult]:
      try:
          results = ribovore.parse_directory(directory)
          return {p.target: p for p in results if p.status != 'FAIL'}
      except ValueError as e:
          if not allow_missing:
              raise ValueError("No ribovore result file in: %s " % directory)
          return {}
  
subject: Fix variable name