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
  
  from click.testing import CliRunner
  
  from rnacentral_pipeline.cli import qa
  
  
  def test_can_parse_rfam_output():
      runner = CliRunner()
      filename = os.path.abspath('data/qa/rfam/scan.tbl')
      with runner.isolated_filesystem():
          result = runner.invoke(qa.cli, ['rfam', filename, 'rfam.csv'])
          assert result.exit_code == 0
          assert not result.exception
  
          with open('rfam.csv', 'r') as raw:
              data = raw.readlines()
              assert len(data) == 129
  
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
  
  from click.testing import CliRunner
  
  from rnacentral_pipeline.cli import qa
  
  
  def test_can_parse_rfam_output():
      runner = CliRunner()
      filename = os.path.abspath('data/qa/rfam/scan.tbl')
      with runner.isolated_filesystem():
          result = runner.invoke(qa.cli, ['rfam', filename, 'rfam.csv'])
          assert result.exit_code == 0
          assert not result.exception
  
          with open('rfam.csv', 'r') as raw:
              data = raw.readlines()
              assert len(data) == 126
  
subject: Validate correct count