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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.
"""
This module provides code to access resources at ExPASy over the WWW.
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_sprot_raw Interface to the get-sprot-raw.pl CGI script.
sprot_search_ful Interface to the sprot-search-ful CGI script.
sprot_search_de Interface to the sprot-search-de CGI script.
_open
"""
import time
import urllib
from Bio import File
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.
"""
# XXX need to check to see if the entry exists!
return _open("%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.
"""
# XXX need to check to see if the entry exists!
return _open("%s?%s" % (cgi, id))
def get_sprot_raw(id, cgi='http://www.expasy.ch/cgi-bin/get-sprot-raw.pl'):
"""get_sprot_raw(id, cgi='http://www.expasy.ch/cgi-bin/get-sprot-raw.pl')
-> handle
Get a handle to a raw SwissProt entry at ExPASy.
"""
return _open("%s?%s" % (cgi, 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'
return _open(cgi, variables)
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'
return _open(cgi, variables)
def scanprosite1(seq=None, id=None, exclude_frequent=None,
cgi='http://expasy.cbr.nrc.ca/cgi-bin/scanprosite/scanprosite?1'):
"""scanprosite1(seq=None, id=None, exclude_frequent=None,
cgi='http://expasy.cbr.nrc.ca/cgi-bin/scanprosite/scanprosite?1') -> handle
Scan a sequence for a Prosite pattern. Either a sequence or a SwissProt/
trEMBL sequence can be passed. exclude_frequent specifies whether to
exclude patterns with high probability.
"""
variables = {}
if seq:
variables['SEQ'] = seq
if id:
variables['ID'] = id
if exclude_frequent:
variables['box'] = 'ok'
return _open(cgi, variables, get=0)
def _open(cgi, params={}, get=1):
"""_open(cgi, params={}, get=1) -> UndoHandle
Open a handle to ExPASy. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. get is a boolean
that describes whether a GET should be used. Does some
simple error checking, and will raise an IOError if it encounters one.
"""
# Open a handle to ExPASy.
options = urllib.urlencode(params)
if get: # do a GET
fullcgi = cgi
if options:
fullcgi = "%s?%s" % (cgi, options)
handle = urllib.urlopen(fullcgi)
else: # do a POST
handle = urllib.urlopen(cgi, options)
# Wrap the handle inside an UndoHandle.
uhandle = File.UndoHandle(handle)
# If the key doesn't exist, ExPASy returns nothing.
if not uhandle.peekline():
raise IOError, "no results"
return uhandle
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