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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
139 lines
4.3 KiB
Python
139 lines
4.3 KiB
Python
# Copyright 2000 by Jeffrey Chang. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Code to access resources at ExPASy over the WWW.
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See https://www.expasy.org/
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Functions:
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- get_prodoc_entry Interface to the get-prodoc-entry CGI script.
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- get_prosite_entry Interface to the get-prosite-entry CGI script.
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- get_prosite_raw Interface to the get-prosite-raw CGI script.
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- get_sprot_raw Interface to the get-sprot-raw CGI script.
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"""
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import io
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from urllib.error import HTTPError
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from urllib.request import urlopen
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def get_prodoc_entry(
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id, cgi="https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry"
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):
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"""Get a text handle to a PRODOC entry at ExPASy in HTML format.
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>>> from Bio import ExPASy
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>>> import os
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>>> with ExPASy.get_prodoc_entry('PDOC00001') as in_handle:
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... html = in_handle.read()
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...
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>>> with open("myprodocrecord.html", "w") as out_handle:
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... length = out_handle.write(html)
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...
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>>> os.remove("myprodocrecord.html") # tidy up
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For a non-existing key XXX, ExPASy returns an HTML-formatted page
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containing this text: 'There is currently no PROSITE entry for'
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"""
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return _open(f"{cgi}?{id}")
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def get_prosite_entry(
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id, cgi="https://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry"
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):
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"""Get a text handle to a PROSITE entry at ExPASy in HTML format.
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>>> from Bio import ExPASy
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>>> import os
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>>> with ExPASy.get_prosite_entry('PS00001') as in_handle:
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... html = in_handle.read()
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...
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>>> with open("myprositerecord.html", "w") as out_handle:
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... length = out_handle.write(html)
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...
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>>> os.remove("myprositerecord.html") # tidy up
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For a non-existing key XXX, ExPASy returns an HTML-formatted page
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containing this text: 'There is currently no PROSITE entry for'
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"""
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return _open(f"{cgi}?{id}")
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def get_prosite_raw(id, cgi=None):
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"""Get a text handle to a raw PROSITE or PRODOC record at ExPASy.
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The cgi argument is deprecated due to changes in the ExPASy
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website.
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>>> from Bio import ExPASy
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>>> from Bio.ExPASy import Prosite
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>>> with ExPASy.get_prosite_raw('PS00001') as handle:
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... record = Prosite.read(handle)
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...
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>>> print(record.accession)
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PS00001
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This function raises a ValueError if the identifier does not exist:
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>>> handle = ExPASy.get_prosite_raw("DOES_NOT_EXIST")
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Traceback (most recent call last):
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...
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ValueError: Failed to find entry 'DOES_NOT_EXIST' on ExPASy
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"""
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try:
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handle = _open(f"https://prosite.expasy.org/{id}.txt")
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except HTTPError as exception:
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if exception.code == 404:
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raise ValueError("Failed to find entry '%s' on ExPASy" % id) from None
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else:
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raise
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# This has happened historically, redirected to main page:
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if handle.url == "https://www.expasy.org/":
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raise ValueError(f"Failed to find entry '{id}' on ExPASy") from None
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return handle
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def get_sprot_raw(id):
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"""Get a text handle to a raw SwissProt entry at ExPASy.
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For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt
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(as per the https://www.expasy.org/expasy_urls.html documentation).
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>>> from Bio import ExPASy
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>>> from Bio import SwissProt
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>>> with ExPASy.get_sprot_raw("O23729") as handle:
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... record = SwissProt.read(handle)
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...
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>>> print(record.entry_name)
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CHS3_BROFI
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This function raises a ValueError if the identifier does not exist:
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>>> ExPASy.get_sprot_raw("DOES_NOT_EXIST")
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Traceback (most recent call last):
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...
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ValueError: Failed to find SwissProt entry 'DOES_NOT_EXIST'
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"""
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try:
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handle = _open(f"http://www.uniprot.org/uniprot/{id}.txt")
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except HTTPError as exception:
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if exception.code in (400, 404):
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raise ValueError(f"Failed to find SwissProt entry '{id}'") from None
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else:
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raise
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return handle
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def _open(url):
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"""Open URL and convert to text assuming UTF-8 encoding (PRIVATE)."""
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handle = urlopen(url)
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text_handle = io.TextIOWrapper(handle, encoding="UTF-8")
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text_handle.url = handle.url
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return text_handle
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