old_contents: #!/usr/bin/env python
  # Description = Download UniProt based proteome data for a taxonomy id
  # author= "Malvika Sharan <malvika.sharan@uni-wuerzburg.de>"
  # email = "malvika.sharan@uni-wuerzburg.de"
  # 2016-05-20
  
  import sys
  try:
      from urllib.request import urlopen
  except ImportError:
      print('Python package urllib is missing. Please install/update.\n')
      sys.exit(0)
  
  
  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)
  
new_contents: #!/usr/bin/env python
  # Description = Download UniProt based proteome data for a taxonomy id
  
  import sys
  try:
      from urllib.request import urlopen
  except ImportError:
      print('Python package urllib is missing. Please install/update.\n')
      sys.exit(0)
  
  
  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)
  
subject: Update uniprot_proteome_table.py