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 os
  
  import luigi
  
  from tasks.config import rgd
  from tasks.config import output
  from tasks.utils.entry_writers import Output
  from tasks.utils.fetch import Fetch as FetchTask
  
  from databases.rgd import parsers
  from databases.rgd import helpers
  
  
  class RgdOrganism(luigi.Task):
      organism = luigi.Parameter()
  
      def requires(self):
          conf = rgd()
          summary = helpers.RgdInfo.from_name(self.organism)
          local_genes = conf.raw(self.organism + '-genes.txt')
          local_sequences = conf.raw(self.organism + 'sequences.fasta')
          return [
              FetchTask(
                  remote_path=summary.sequence_uri(conf),
                  local_path=local_sequences,
              ),
              FetchTask(
                  remote_path=summary.gene_uri(conf),
                  local_path=local_genes,
              ),
          ]
  
      def output(self):
          prefix = os.path.basename(self.organism)
          return Output.build(output().base, 'rgd', prefix)
  
      def run(self):
          extract, fetch = self.requires()
          genes_file = fetch.output().fn
          seqs_file = extract.output().fn
  
          with self.output().writer() as writer:
              with helpers.indexed(seqs_file) as indexed, \
                      open(genes_file, 'r') as handle:
  
                  writer.write_all(parsers.parse(handle, indexed))
  
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 os
  
  import luigi
  
  from tasks.config import rgd
  from tasks.config import output
  from tasks.utils.entry_writers import Output
  from tasks.utils.fetch import FetchTask
  
  from databases.rgd import parsers
  from databases.rgd import helpers
  
  
  class RgdOrganism(luigi.Task):
      organism = luigi.Parameter()
  
      def requires(self):
          conf = rgd()
          summary = helpers.RgdInfo.from_name(self.organism)
          local_genes = conf.raw(self.organism + '-genes.txt')
          local_sequences = conf.raw(self.organism + 'sequences.fasta')
          return [
              FetchTask(
                  remote_path=summary.sequence_uri(conf),
                  local_path=local_sequences,
              ),
              FetchTask(
                  remote_path=summary.gene_uri(conf),
                  local_path=local_genes,
              ),
          ]
  
      def output(self):
          prefix = os.path.basename(self.organism)
          return Output.build(output().base, 'rgd', prefix)
  
      def run(self):
          extract, fetch = self.requires()
          genes_file = fetch.output().fn
          seqs_file = extract.output().fn
  
          with self.output().writer() as writer:
              with helpers.indexed(seqs_file) as indexed, \
                      open(genes_file, 'r') as handle:
  
                  writer.write_all(parsers.parse(handle, indexed))
  
subject: Correct import