old_contents: # -*- coding: utf-8 -*-
  from __future__ import absolute_import
  from __future__ import print_function
  from __future__ import unicode_literals
  
  import click
  from flask.cli import with_appcontext
  from flask import current_app
  
  
  click.disable_unicode_literals_warning = True
  
  import os
  
  
  @click.group()
  def pfamscan():
      """PfamScan commands"""
      pass
  
  
  def run(cmds, **kwargs):
      cmd = ' && '.join(['({:})'.format(c) for c in cmds]).format(**kwargs)
      click.echo("Running:\n{}".format(cmd))
      os.system(cmd)
  
  
  @pfamscan.command()
  def install():
      """Download and compile pfamscan sourcecode."""
      cmds = [
          'wget -c http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz',
          'tar xvzf PfamScan.tar.gz',
          'sudo perl - MCPAN - e"install Moose"'
      ]
      run(cmds)
  
  
  @pfamscan.command()
  @click.option('--version', '-v', 'version',
                type=click.STRING,
                multiple=False,
                default='31.0',
                help='Version to download.')
  @click.option('--ftp',
                is_flag=True,
                help='Force to use ftp.')
  def index(version, ftp):
      """Download PfamA-full file."""
      protocol = 'ftp' if ftp else 'http'
      cmds = [
          'wget -c {protocol}://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam{version}/Pfam-A.hmm.gz -O ./Pfam{version}/Pfam-A.hmm.gz',
          'wget -c {protocol}://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam{version}/Pfam-A.hmm.dat.gz -O ./Pfam{version}/Pfam-A.hmm.dat.gz',
          'gunzip -c ./Pfam{version}/Pfam-A.hmm.gz > ./Pfam{version}/Pfam-A.hmm',
          'gunzip -c ./Pfam{version}/Pfam-A.hmm.dat.gz > ./Pfam{version}/Pfam-A.hmm.dat',
          './hmmpress ./Pfam{version}/Pfam-A.hmm',
          'mkdir -p tmp',
  
      ]
      run(cmds, version=version, protocol=protocol)
  
new_contents: # -*- coding: utf-8 -*-
  from __future__ import absolute_import
  from __future__ import print_function
  from __future__ import unicode_literals
  
  import click
  from flask.cli import with_appcontext
  from flask import current_app
  
  
  click.disable_unicode_literals_warning = True
  
  import os
  
  
  @click.group()
  def pfamscan():
      """PfamScan commands"""
      pass
  
  
  def run(cmds, **kwargs):
      cmd = ' && '.join(['({:})'.format(c) for c in cmds]).format(**kwargs)
      click.echo("Running:\n{}".format(cmd))
      os.system(cmd)
  
  
  @pfamscan.command()
  def install():
      """Download and compile pfamscan sourcecode."""
      cmds = [
          'wget -c http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz',
          'tar xvzf PfamScan.tar.gz',
          'sudo perl - MCPAN - e"install Moose"'
      ]
      run(cmds)
  
  
  @pfamscan.command()
  @click.option('--version', '-v', 'version',
                type=click.STRING,
                multiple=False,
                default='31.0',
                help='Version to download.')
  @click.option('--ftp',
                is_flag=True,
                help='Force to use ftp.')
  def index(version, ftp):
      """Download PfamA-full file."""
      protocol = 'ftp' if ftp else 'http'
      cmds = [
          'mkdir -p ./Pfam{version}',
          'wget -c {protocol}://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam{version}/Pfam-A.hmm.gz -O ./Pfam{version}/Pfam-A.hmm.gz',
          'wget -c {protocol}://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam{version}/Pfam-A.hmm.dat.gz -O ./Pfam{version}/Pfam-A.hmm.dat.gz',
          'gunzip -c ./Pfam{version}/Pfam-A.hmm.gz > ./Pfam{version}/Pfam-A.hmm',
          'gunzip -c ./Pfam{version}/Pfam-A.hmm.dat.gz > ./Pfam{version}/Pfam-A.hmm.dat',
          './hmmpress ./Pfam{version}/Pfam-A.hmm',
          'mkdir -p tmp',
  
      ]
      run(cmds, version=version, protocol=protocol)
  
subject: Fix bug in pfamscan command.