Package Bio :: Package ExPASy
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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 -def get_prosite_entry(id, 38 cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry'):
39 """get_prosite_entry(id, 40 cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry') -> handle 41 42 Get a handle to a PROSITE entry at ExPASy in HTML format. 43 44 For a non-existing key XXX, ExPASy returns an HTML-formatted page 45 containing this line: 46 'There is currently no PROSITE entry for XXX. Please try again.' 47 """ 48 handle = urllib.urlopen("%s?%s" % (cgi, id)) 49 return handle
50
51 -def get_prosite_raw(id, cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl'):
52 """get_prosite_raw(id, 53 cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl') 54 -> handle 55 56 Get a handle to a raw PROSITE or PRODOC entry at ExPASy. 57 58 For a non-existing key, ExPASy returns nothing. 59 """ 60 handle = urllib.urlopen("%s?%s" % (cgi, id)) 61 return handle
62
63 -def get_sprot_raw(id):
64 """Get a handle to a raw SwissProt entry at ExPASy. 65 66 For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt 67 (as per the http://www.expasy.ch/expasy_urls.html documentation). 68 """ 69 return urllib.urlopen("http://www.uniprot.org/uniprot/%s.txt" % id)
70
71 -def sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None, 72 cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful'):
73 """sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None, 74 cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful') -> handle 75 76 Search SwissProt by full text. 77 78 """ 79 variables = {'SEARCH' : text} 80 if make_wild: 81 variables['makeWild'] = 'on' 82 if swissprot: 83 variables['S'] = 'on' 84 if trembl: 85 variables['T'] = 'on' 86 options = urllib.urlencode(variables) 87 fullcgi = "%s?%s" % (cgi, options) 88 handle = urllib.urlopen(fullcgi) 89 return handle
90
91 -def sprot_search_de(text, swissprot=1, trembl=None, 92 cgi='http://www.expasy.ch/cgi-bin/sprot-search-de'):
93 """sprot_search_de(text, swissprot=1, trembl=None, 94 cgi='http://www.expasy.ch/cgi-bin/sprot-search-de') -> handle 95 96 Search SwissProt by name, description, gene name, species, or 97 organelle. 98 99 """ 100 variables = {'SEARCH' : text} 101 if swissprot: 102 variables['S'] = 'on' 103 if trembl: 104 variables['T'] = 'on' 105 options = urllib.urlencode(variables) 106 fullcgi = "%s?%s" % (cgi, options) 107 handle = urllib.urlopen(fullcgi) 108 return handle
109