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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 https://www.expasy.org/
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.
"""
import io
from urllib.request import urlopen
from urllib.error import HTTPError
def get_prodoc_entry(
id, cgi="https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry"
):
"""Get a text handle to a PRODOC entry at ExPASy in HTML format.
>>> from Bio import ExPASy
>>> import os
>>> with ExPASy.get_prodoc_entry('PDOC00001') as in_handle:
... html = in_handle.read()
...
>>> with open("myprodocrecord.html", "w") as out_handle:
... length = out_handle.write(html)
...
>>> os.remove("myprodocrecord.html") # tidy up
For a non-existing key XXX, ExPASy returns an HTML-formatted page
containing this text: 'There is currently no PROSITE entry for'
"""
return _open(f"{cgi}?{id}")
def get_prosite_entry(
id, cgi="https://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry"
):
"""Get a text handle to a PROSITE entry at ExPASy in HTML format.
>>> from Bio import ExPASy
>>> import os
>>> with ExPASy.get_prosite_entry('PS00001') as in_handle:
... html = in_handle.read()
...
>>> with open("myprositerecord.html", "w") as out_handle:
... length = out_handle.write(html)
...
>>> os.remove("myprositerecord.html") # tidy up
For a non-existing key XXX, ExPASy returns an HTML-formatted page
containing this text: 'There is currently no PROSITE entry for'
"""
return _open(f"{cgi}?{id}")
def get_prosite_raw(id, cgi=None):
"""Get a text handle to a raw PROSITE or PRODOC record at ExPASy.
The cgi argument is deprecated due to changes in the ExPASy
website.
>>> from Bio import ExPASy
>>> from Bio.ExPASy import Prosite
>>> with ExPASy.get_prosite_raw('PS00001') as handle:
... record = Prosite.read(handle)
...
>>> print(record.accession)
PS00001
This function raises a ValueError if the identifier does not exist:
>>> handle = ExPASy.get_prosite_raw("DOES_NOT_EXIST")
Traceback (most recent call last):
...
ValueError: Failed to find entry 'DOES_NOT_EXIST' on ExPASy
"""
handle = _open(f"https://prosite.expasy.org/{id}.txt")
if handle.url == "https://www.expasy.org/":
raise ValueError(f"Failed to find entry '{id}' on ExPASy") from None
return handle
def get_sprot_raw(id):
"""Get a text handle to a raw SwissProt entry at ExPASy.
For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt
(as per the https://www.expasy.org/expasy_urls.html documentation).
>>> from Bio import ExPASy
>>> from Bio import SwissProt
>>> with ExPASy.get_sprot_raw("O23729") as handle:
... record = SwissProt.read(handle)
...
>>> print(record.entry_name)
CHS3_BROFI
This function raises a ValueError if the identifier does not exist:
>>> ExPASy.get_sprot_raw("DOES_NOT_EXIST")
Traceback (most recent call last):
...
ValueError: Failed to find SwissProt entry 'DOES_NOT_EXIST'
"""
try:
handle = _open(f"http://www.uniprot.org/uniprot/{id}.txt")
except HTTPError as exception:
if exception.code in (400, 404):
raise ValueError(f"Failed to find SwissProt entry '{id}'") from None
else:
raise
return handle
def _open(url):
"""Open URL and convert to text assuming UTF-8 encoding (PRIVATE)."""
handle = urlopen(url)
text_handle = io.TextIOWrapper(handle, encoding="UTF-8")
text_handle.url = handle.url
return text_handle
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