Source Code for Package Bio.ExPASy

  1  # Copyright 2000 by Jeffrey Chang.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5   
  6  """ 
  7  This module provides code to access resources at ExPASy over the WWW. 
  8  http://www.expasy.ch/ 
  9   
 10   
 11  Functions: 
 12  get_prodoc_entry  Interface to the get-prodoc-entry CGI script. 
 13  get_prosite_entry Interface to the get-prosite-entry CGI script. 
 14  get_prosite_raw   Interface to the get-prosite-raw CGI script. 
 15  get_sprot_raw     Interface to the get-sprot-raw CGI script. 
 16  sprot_search_ful  Interface to the sprot-search-ful CGI script. 
 17  sprot_search_de   Interface to the sprot-search-de CGI script. 
 18  """ 
 19   
 20  import urllib 
 21   
 22   
 23 -def get_prodoc_entry(id, cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry'): 
 24      """get_prodoc_entry(id, 
 25      cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry') -> handle 
 26   
 27      Get a handle to a PRODOC entry at ExPASy in HTML format. 
 28   
 29      For a non-existing key XXX, ExPASy returns an HTML-formatted page 
 30      containing this line: 
 31      'There is no PROSITE documentation entry XXX. Please try again.' 
 32      """ 
 33      # Open a handle to ExPASy. 
 34      handle = urllib.urlopen("%s?%s" % (cgi, id)) 
 35      return handle 
 36   
 37   
 38 -def get_prosite_entry(id, 
 39                        cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry'): 
 40      """get_prosite_entry(id, 
 41      cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry') -> handle 
 42   
 43      Get a handle to a PROSITE entry at ExPASy in HTML format. 
 44   
 45      For a non-existing key XXX, ExPASy returns an HTML-formatted page 
 46      containing this line: 
 47      'There is currently no PROSITE entry for XXX. Please try again.' 
 48      """ 
 49      handle = urllib.urlopen("%s?%s" % (cgi, id)) 
 50      return handle 
 51   
 52   
 53 -def get_prosite_raw(id, cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl'): 
 54      """get_prosite_raw(id, 
 55                         cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl') 
 56      -> handle 
 57   
 58      Get a handle to a raw PROSITE or PRODOC entry at ExPASy. 
 59   
 60      For a non-existing key, ExPASy returns nothing. 
 61      """ 
 62      handle = urllib.urlopen("%s?%s" % (cgi, id)) 
 63      return handle 
 64   
 65   
 66 -def get_sprot_raw(id): 
 67      """Get a handle to a raw SwissProt entry at ExPASy. 
 68   
 69      For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt 
 70      (as per the http://www.expasy.ch/expasy_urls.html documentation). 
 71      """ 
 72      return urllib.urlopen("http://www.uniprot.org/uniprot/%s.txt" % id) 
 73   
 74   
 75 -def sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None, 
 76                       cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful'): 
 77      """sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None, 
 78      cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful') -> handle 
 79   
 80      Search SwissProt by full text. 
 81   
 82      """ 
 83      variables = {'SEARCH': text} 
 84      if make_wild: 
 85          variables['makeWild'] = 'on' 
 86      if swissprot: 
 87          variables['S'] = 'on' 
 88      if trembl: 
 89          variables['T'] = 'on' 
 90      options = urllib.urlencode(variables) 
 91      fullcgi = "%s?%s" % (cgi, options) 
 92      handle = urllib.urlopen(fullcgi) 
 93      return handle 
 94   
 95   
 96 -def sprot_search_de(text, swissprot=1, trembl=None, 
 97                      cgi='http://www.expasy.ch/cgi-bin/sprot-search-de'): 
 98      """sprot_search_de(text, swissprot=1, trembl=None, 
 99      cgi='http://www.expasy.ch/cgi-bin/sprot-search-de') -> handle 
100   
101      Search SwissProt by name, description, gene name, species, or 
102      organelle. 
103   
104      """ 
105      variables = {'SEARCH': text} 
106      if swissprot: 
107          variables['S'] = 'on' 
108      if trembl: 
109          variables['T'] = 'on' 
110      options = urllib.urlencode(variables) 
111      fullcgi = "%s?%s" % (cgi, options) 
112      handle = urllib.urlopen(fullcgi) 
113      return handle 
114