old_contents: #!/usr/bin/env python
  """Setup the aTRAM environment."""
  
  # Test pip
  # 1) Clean the /dist directory
  # 2) python3 setup.py sdist bdist_wheel
  # 3) pip install --index-url https://test.pypi.org/simple/
  #    --extra-index-url https://pypi.org/simple atram
  # 4) twine upload --repository-url https://test.pypi.org/legacy/ dist/*
  
  import re
  from setuptools import setup, find_packages
  
  
  def readme():
      """Get README.md content."""
      with open("README.md", 'r') as f:
          return f.read()
      return None
  
  
  def license():
      """Get LICENSE.txt content."""
      with open("LICENSE.txt", 'r') as f:
          return f.read()
      return None
  
  
  def find_version():
      """Read version from db.py."""
      regex = r"^ATRAM_VERSION = ['\"]v?([^'\"]*)['\"]"
      with open("./lib/db.py", 'r') as f:
          match = re.search(regex, f.read(), re.M)
          if match:
              return match.group(1)
  
      raise RuntimeError("Unable to find version string.")
  
  
  def find_requirements():
      """Read requirements.txt file and returns list of requirements."""
      with open("requirements.txt", 'r') as f:
          return f.read().splitlines()
  
      raise RuntimeError("Unable to list requirements.")
  
  
  setup(
      name="atram",
      version=find_version(),
      packages=find_packages(),
      install_requires=find_requirements(),
      description="""atram ("automated target restricted assembly method") is
                     an iterative assembler that performs reference-guided
                     local de novo assemblies using a variety of available
                     methods""",
      long_description=readme(),
      license=license(),
      url="https://github.com/juliema/aTRAM",
      python_requires='>=3.4',
      scripts=['atram/atram.py', 'atram/atram_preprocessor.py'])
  
new_contents: #!/usr/bin/env python
  """Setup the aTRAM environment."""
  
  # Test pip
  # 1) Clean the /dist directory
  # 2) python3 setup.py sdist bdist_wheel
  # 3) pip install --index-url https://test.pypi.org/simple/
  #    --extra-index-url https://pypi.org/simple atram
  # 4) twine upload --repository-url https://test.pypi.org/legacy/ dist/*
  
  import re
  from setuptools import setup, find_packages
  
  
  def readme():
      """Get README.md content."""
      with open("README.md", 'r') as f:
          return f.read()
      return None
  
  
  def license():
      """Get LICENSE.txt content."""
      with open("LICENSE.txt", 'r') as f:
          return f.read()
      return None
  
  
  def find_version():
      """Read version from db.py."""
      regex = r"^ATRAM_VERSION = ['\"]v?([^'\"]*)['\"]"
      with open("./lib/db.py", 'r') as f:
          match = re.search(regex, f.read(), re.M)
          if match:
              return match.group(1)
  
      raise RuntimeError("Unable to find version string.")
  
  
  def find_requirements():
      """Read requirements.txt file and returns list of requirements."""
      with open("requirements.txt", 'r') as f:
          return f.read().splitlines()
  
      raise RuntimeError("Unable to list requirements.")
  
  
  setup(
      name="atram",
      version=find_version(),
      packages=find_packages(),
      install_requires=find_requirements(),
      description="""atram ("automated target restricted assembly method") is
                     an iterative assembler that performs reference-guided
                     local de novo assemblies using a variety of available
                     methods""",
      long_description=readme(),
      license=license(),
      url="https://github.com/juliema/aTRAM",
      python_requires='>=3.4',
      scripts=[
          'atram/atram.py', 
          'atram/atram_preprocessor.py', 
          'atram/atram_stitcher.py'])
  
subject: Add the stitcher to the setup utility