old_contents: #!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  
  from distutils.core import setup
  from distutils.command.install import install as DistutilsInstall
  import os
  import sys
  import subprocess
  
  if sys.version_info < (3, 5):
      print("At least Python 3.5 is required.\n", file=sys.stderr)
      exit(1)
  
  def compile_seqtk():
      """Compiling the seqtk toolkit"""
      old_wd = os.getcwd()
      new_wd = os.path.join(old_wd,"mapdamage","seqtk")
      os.chdir(new_wd)
      if not os.path.isfile("seqtk.c"):
          raise SystemExit("Cannot find seqtk.c")
      if (os.path.isfile("seqtk")):
          os.system("rm seqtk")
      xs = os.system("make -f Makefile")
      os.chdir(old_wd)
      if (xs != 0):
          raise SystemExit("Cannot compile seqtk")
  
  
  def setup_version():
      if not os.path.exists(".git"):
          # Release version, no .git folder
          return
  
      try:
          version = subprocess.check_output(("git", "describe", "--always", "--tags", "--dirty"))
          with open(os.path.join("mapdamage", "_version.py"), "w") as handle:
              handle.write("#!/usr/bin/env python\n")
              handle.write("__version__ = %r\n" % (version.strip(),))
      except (subprocess.CalledProcessError, OSError) as error:
          raise SystemExit("Could not determine mapDamage version: %s" % (error,))
  
  
  class compileInstall(DistutilsInstall):
      # extension of the class to account for an extra compiling step
      def run(self):
          self.record=""
          setup_version()
          compile_seqtk()
          DistutilsInstall.run(self)
          # fixing the permission problem of seqtk
          files = self.get_outputs()
          for fi in files:
              if fi.endswith("seqtk/seqtk"):
                  os.chmod(fi,0o755)
  
  
  
  
  
  setup(
      cmdclass={'install': compileInstall},
      name='mapdamage',
      version='2.2.0',
      author='AurÃ©lien Ginolhac, Mikkel Schubert, Ãkon JÃ³nsson',
      author_email='MSchubert@snm.ku.dk, jonsson.hakon@gmail.com',
      packages=['mapdamage'],
      package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R','tests/*','seqtk/seqtk']},
      scripts=['bin/mapDamage'],
      url='https://github.com/ginolhac/mapDamage',
      license='LICENSE.txt',
      description='mapDamage tracks and quantify DNA damage pattern among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms',
      long_description=open('README.md').read()
  )
  
new_contents: #!/usr/bin/env python3
  # -*- coding: utf-8 -*-
  
  from distutils.core import setup
  from distutils.command.install import install as DistutilsInstall
  import os
  import sys
  import subprocess
  
  if sys.version_info < (3, 5):
      print("At least Python 3.5 is required.\n", file=sys.stderr)
      exit(1)
  
  def compile_seqtk():
      """Compiling the seqtk toolkit"""
      old_wd = os.getcwd()
      new_wd = os.path.join(old_wd,"mapdamage","seqtk")
      os.chdir(new_wd)
      if not os.path.isfile("seqtk.c"):
          raise SystemExit("Cannot find seqtk.c")
      if (os.path.isfile("seqtk")):
          os.system("rm seqtk")
      xs = os.system("make -f Makefile")
      os.chdir(old_wd)
      if (xs != 0):
          raise SystemExit("Cannot compile seqtk")
  
  
  def setup_version():
      if not os.path.exists(".git"):
          # Release version, no .git folder
          return
  
      try:
          version = subprocess.check_output(("git", "describe", "--always", "--tags", "--dirty"))
          with open(os.path.join("mapdamage", "_version.py"), "w") as handle:
              handle.write("#!/usr/bin/env python\n")
              handle.write("__version__ = %r\n" % (version.decode("utf-8").strip(),))
      except (subprocess.CalledProcessError, OSError) as error:
          raise SystemExit("Could not determine mapDamage version: %s" % (error,))
  
  
  class compileInstall(DistutilsInstall):
      # extension of the class to account for an extra compiling step
      def run(self):
          self.record=""
          setup_version()
          compile_seqtk()
          DistutilsInstall.run(self)
          # fixing the permission problem of seqtk
          files = self.get_outputs()
          for fi in files:
              if fi.endswith("seqtk/seqtk"):
                  os.chmod(fi,0o755)
  
  
  
  
  
  setup(
      cmdclass={'install': compileInstall},
      name='mapdamage',
      version='2.2.0',
      author='AurÃ©lien Ginolhac, Mikkel Schubert, Ãkon JÃ³nsson',
      author_email='MSchubert@snm.ku.dk, jonsson.hakon@gmail.com',
      packages=['mapdamage'],
      package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R','tests/*','seqtk/seqtk']},
      scripts=['bin/mapDamage'],
      url='https://github.com/ginolhac/mapDamage',
      license='LICENSE.txt',
      description='mapDamage tracks and quantify DNA damage pattern among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms',
      long_description=open('README.md').read()
  )
  
subject: Fix --version command-line option.