old_contents: # Download file utility
  
  
  def download_file(base_url, filename, download_dir):
      """
      Check if file is already downloaded, and download if not
  
      Parameters:
      base_url: the base http address of file to download
      filename: the file located at the base_url (will be name of download)
      download_dir: the location to save fh
  
      Output:
      Nothing - will save base_url/fh to download_dir/fh
      """
      import os
      from urllib.request import urlretrieve
  
      path = os.path.join(download_dir, filename)
      if not (os.path.exists(path)):
          urlretrieve(base_url + filename, path)
  
  
  def process_repeats(base_dir, filename, genome):
      """
      Process the irregularly structured repeatmasker file
      """
      from subprocess import call
  
      full_loc = base_dir + filename
      call(['gunzip', full_loc])
  
      # Replace variable length space delimiters with tabs and output tsv file
      CMD = "sed 's/ \+/\\t/g' " + full_loc[:-3] + " > " + full_loc[:-3] + ".tsv"
      call(CMD, shell=True)
  
new_contents: # Download file utility
  
  
  def download_file(base_url, filename, download_dir):
      """
      Check if file is already downloaded, and download if not
  
      Parameters:
      base_url: the base http address of file to download
      filename: the file located at the base_url (will be name of download)
      download_dir: the location to save fh
  
      Output:
      Nothing - will save base_url/fh to download_dir/fh
      """
      import os
      from urllib.request import urlretrieve
  
      path = os.path.join(download_dir, filename)
      if not (os.path.exists(path)):
          urlretrieve(base_url + filename, path)
  
  
  def process_repeats(base_dir, filename, genome):
      """
      Process the irregularly structured repeatmasker file
      """
      from subprocess import call
  
      full_loc = base_dir + filename
      call(['gunzip', full_loc])
  
      # Replace variable length space delimiters with tabs and output tsv file
      CMD = "sed 's/ \+/\\t/g' " + full_loc[:-3] + " > " + full_loc[:-3] + ".tsv"
      call(CMD, shell=True)
  
  
  def untar_mouse_domain(tar_file):
      """
      Mouse domains are downloaded as a tar archive - extracts contents
      """
      import tarfile
  
      tar = tarfile.open(tar_file)
      tar.extractall()
  
subject: add function to untar mouse TAD domains