old_contents: #!/usr/bin/env python 
  
  import sys
  try:
      import urllib.request
      from urllib.request import urlopen
  except ImportError:
      print('Python package urllib is missing. Please install/update.\n'
      'Please ignore if you are only testing the example provided by APRICOT')
  
  __description__ = "Downloads the complete proteome data from UniProt."
  __author__ = "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  __email__ = "malvika.sharan@uni-wuerzburg.de"
  
  def format_uniprot_table(proteome_table, uniprot_link):
      '''Downloads protein information
      table from UniProt database for
      the selected taxonomy id'''
      try:
          response = urlopen(uniprot_link)
          for entry in str(response.read()).split('\\n'):
              if not entry == "'" and not entry == '"':
                  if not entry.startswith("b'Entry") and not entry.startswith('b"Entry'):
                      proteome_table.write("%s\n" % '\t'.join(list(entry.split('\\t'))))
          print('"\nDownloaded protein information using UniProt link: %s\n"' % (
              uniprot_link))
      except:
          print(
              "UniProt entry is apparently deleted, please check: %s"
              % uniprot_link)
      
  if __name__ == '__main__':
      proteome_table = sys.argv[1]
      uniprot_query = sys.argv[2]
      if "http://www.uniprot.org/" in uniprot_link:
          format_uniprot_table(proteome_table, uniprot_query)
      else:
          try:
              format_uniprot_table(proteome_table, uniprot_query)
          except KeyError:
              print("Please provide query UniProt ids or a taxonomy id for UniProt table retrieval.")
  
new_contents: #!/usr/bin/env python 
  
  import sys
  try:
      import urllib.request
      from urllib.request import urlopen
  except ImportError:
      print('Python package urllib is missing. Please install/update.')
      sys.exit(0)
  
  __description__ = "Downloads the complete proteome data from UniProt."
  __author__ = "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  __email__ = "malvika.sharan@uni-wuerzburg.de"
  
  def format_uniprot_table(proteome_table, uniprot_link):
      '''Downloads protein information
      table from UniProt database for
      the selected taxonomy id'''
      try:
          response = urlopen(uniprot_link)
          for entry in str(response.read()).split('\\n'):
              if not entry == "'" and not entry == '"':
                  if not entry.startswith("b'Entry") and not entry.startswith('b"Entry'):
                      proteome_table.write("%s\n" % '\t'.join(list(entry.split('\\t'))))
          print('"\nDownloaded protein information using UniProt link: %s\n"' % (
              uniprot_link))
      except:
          print(
              "UniProt entry is apparently deleted, please check: %s"
              % uniprot_link)
      
  if __name__ == '__main__':
      proteome_table = sys.argv[1]
      uniprot_query = sys.argv[2]
      if "http://www.uniprot.org/" in uniprot_link:
          format_uniprot_table(proteome_table, uniprot_query)
      else:
          try:
              format_uniprot_table(proteome_table, uniprot_query)
          except KeyError:
              print("Please provide query UniProt ids or a taxonomy id for UniProt table retrieval.")
  
subject: Update uniprot_proteome_table.py