old_contents: #!/usr/bin/env python
  
  # Copyright (c) 2016. Mount Sinai School of Medicine
  #
  # 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 __future__ import print_function, division, absolute_import
  import logging
  import logging.config
  import pkg_resources
  
  from isovar.cli.variant_sequences import (
      make_variant_sequences_arg_parser,
      variant_sequences_dataframe_from_args
  )
  
  
  logging.config.fileConfig(pkg_resources.resource_filename(__name__, 'logging.conf'))
  logger = logging.getLogger(__name__)
  
  parser = make_variant_sequences_arg_parser(add_sequence_length_arg=True)
  parser.add_argument(
      "--output",
      default="isovar-variant-sequences-results.csv",
      help="Name of CSV file which contains predicted sequences")
  
  if __name__ == "__main__":
      args = parser.parse_args()
      logger.info(args)
      df = variant_sequences_dataframe_from_args(args)
      logger.info(df)
      df.to_csv(args.output)
  
new_contents: #!/usr/bin/env python
  
  # Copyright (c) 2016. Mount Sinai School of Medicine
  #
  # 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 __future__ import print_function, division, absolute_import
  import logging
  import logging.config
  import pkg_resources
  
  from isovar.cli.variant_sequences import (
      make_variant_sequences_arg_parser,
      variant_sequences_dataframe_from_args
  )
  
  
  logging.config.fileConfig(pkg_resources.resource_filename('isovar.cli', 'logging.conf'))
  logger = logging.getLogger(__name__)
  
  parser = make_variant_sequences_arg_parser(add_sequence_length_arg=True)
  parser.add_argument(
      "--output",
      default="isovar-variant-sequences-results.csv",
      help="Name of CSV file which contains predicted sequences")
  
  if __name__ == "__main__":
      args = parser.parse_args()
      logger.info(args)
      df = variant_sequences_dataframe_from_args(args)
      logger.info(df)
      df.to_csv(args.output)
  
subject: Fix logging.conf loading