old_contents: #!/usr/bin/env python
  
  # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2020] 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.
  """
  
  from os.path import getsize
  
  import click
  
  from Bio import SeqIO
  
  
  def records(filename):
      for record in SeqIO.parse(filename, "embl"):
          if 'metagenome' in lineage(record).lower():
              yield record
  
  
  @click.command()
  @click.argument('filename', type=click.File('r'))
  @click.argument('output', type=click.File('w'))
  def main(filename, output):
      """
      Convert a ENA EMBL file into a fasta file suitable for ribotyper analysis.
      """
      SeqIO.write(sequences(filename), output, "fasta")
      output.flush()
  
      if not getsize(output.name):
          os.remove(output.name)
  
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python
  
  # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2020] 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 os.path import getsize
  
  import click
  
  from Bio import SeqIO
  
  
  def lineage(record) -> str:
      taxonomy = record.annotations.get('taxonomy', [])
      organism = record.annotations.get('organism', '')
      taxonomy.append(organism)
      return '; '.join(taxonomy).lower()
  
  
  def records(filename):
      for record in SeqIO.parse(filename, "embl"):
          if 'metagenome' in lineage(record):
              yield record
  
  
  @click.command()
  @click.argument('filename', type=click.File('r'))
  @click.argument('output', type=click.File('w'))
  def main(filename, output):
      """
      Convert a ENA EMBL file into a fasta file suitable for ribotyper analysis.
      """
      SeqIO.write(records(filename), output, "fasta")
      output.flush()
  
      if not getsize(output.name):
          os.remove(output.name)
  
  
  if __name__ == '__main__':
      main()
  
subject: Fix ena2fasta