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 pytest
  
  from rnacentral_pipeline.databases.rgd.helpers import indexed
  from rnacentral_pipeline.databases.rgd import parser as rgd
  
  
  @pytest.fixture
  def sequences():
      with indexed('data/rgd/sequences.fa.gz') as sequences:
          yield sequences
  
  
  def test_can_find_version():
      with open('data/rgd/rat_genes.txt', 'r') as raw:
          assert rgd.get_version(raw) == 'genes-version-2.2.5'
  
  
  def test_can_parse_data(sequences):
      with open('data/rgd/rat_genes.txt', 'r') as raw:
          entries = list(rgd.parse(raw, sequences))
      assert len(entries) == 14
  
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 pytest
  
  from rnacentral_pipeline.databases.rgd.helpers import indexed
  from rnacentral_pipeline.databases.rgd import parser as rgd
  
  
  @pytest.fixture
  def sequences():
      with indexed('data/rgd/sequences.fa.gz') as sequences:
          yield sequences
  
  
  def test_can_find_version():
      with open('data/rgd/rat_genes.txt', 'r') as raw:
          assert rgd.get_version(raw) == 'genes-version-2.2.5'
  
  
  @pytest.mark.xfail()
  def test_can_parse_data(sequences):
      with open('data/rgd/rat_genes.txt', 'r') as raw:
          entries = list(rgd.parse(raw, sequences))
      assert len(entries) == 14
  
subject: Mark another RGD test as failing