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ExPASy.py
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
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Imported modules
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from Bio import File
import time
import urllib
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Functions
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_open
get_prodoc_entry
get_prosite_entry
get_sprot_raw
scanprosite1
sprot_search_de
sprot_search_ful
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_open
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_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.
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get_prodoc_entry
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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.
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get_prosite_entry
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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.
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get_sprot_raw
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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.
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scanprosite1
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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.
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sprot_search_de
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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.
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sprot_search_ful
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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.
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