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# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code to access resources at ExPASy over the WWW.
See http://www.expasy.ch/
Functions:
- get_prodoc_entry Interface to the get-prodoc-entry CGI script.
- get_prosite_entry Interface to the get-prosite-entry CGI script.
- get_prosite_raw Interface to the get-prosite-raw CGI script.
- get_sprot_raw Interface to the get-sprot-raw CGI script.
- sprot_search_ful Interface to the sprot-search-ful CGI script.
- sprot_search_de Interface to the sprot-search-de CGI script.
"""
# Importing these functions with leading underscore as not intended for reuse
from Bio._py3k import urlopen as _urlopen
from Bio._py3k import urlencode as _urlencode
def get_prodoc_entry(id, cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry'):
"""get_prodoc_entry(id,
cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry') -> handle
Get a handle to a PRODOC entry at ExPASy in HTML format.
For a non-existing key XXX, ExPASy returns an HTML-formatted page
containing this line:
'There is no PROSITE documentation entry XXX. Please try again.'
"""
# Open a handle to ExPASy.
return _urlopen("%s?%s" % (cgi, id))
def get_prosite_entry(id,
cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry'):
"""get_prosite_entry(id,
cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry') -> handle
Get a handle to a PROSITE entry at ExPASy in HTML format.
For a non-existing key XXX, ExPASy returns an HTML-formatted page
containing this line:
'There is currently no PROSITE entry for XXX. Please try again.'
"""
return _urlopen("%s?%s" % (cgi, id))
def get_prosite_raw(id, cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl'):
"""get_prosite_raw(id,
cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl')
-> handle
Get a handle to a raw PROSITE or PRODOC entry at ExPASy.
For a non-existing key, ExPASy returns nothing.
"""
return _urlopen("%s?%s" % (cgi, id))
def get_sprot_raw(id):
"""Get a handle to a raw SwissProt entry at ExPASy.
For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt
(as per the http://www.expasy.ch/expasy_urls.html documentation).
"""
return _urlopen("http://www.uniprot.org/uniprot/%s.txt" % id)
def sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None,
cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful'):
"""sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None,
cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful') -> handle
Search SwissProt by full text.
"""
variables = {'SEARCH': text}
if make_wild:
variables['makeWild'] = 'on'
if swissprot:
variables['S'] = 'on'
if trembl:
variables['T'] = 'on'
options = _urlencode(variables)
fullcgi = "%s?%s" % (cgi, options)
handle = _urlopen(fullcgi)
return handle
def sprot_search_de(text, swissprot=1, trembl=None,
cgi='http://www.expasy.ch/cgi-bin/sprot-search-de'):
"""sprot_search_de(text, swissprot=1, trembl=None,
cgi='http://www.expasy.ch/cgi-bin/sprot-search-de') -> handle
Search SwissProt by name, description, gene name, species, or
organelle.
"""
variables = {'SEARCH': text}
if swissprot:
variables['S'] = 'on'
if trembl:
variables['T'] = 'on'
options = _urlencode(variables)
fullcgi = "%s?%s" % (cgi, options)
handle = _urlopen(fullcgi)
return handle
|
