o Rŀg@sZdZddlZddlmZddlmZ dddZ dd d Zdd d Zd dZ ddZ dS)aeCode 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. N) HTTPError)urlopen;https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entrycCt|d|S)aGet 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' ?_openidcgir G/var/www/html/myenv/lib/python3.10/site-packages/Bio/ExPASy/__init__.pyget_prodoc_entryr>> 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' rrr r r r get_prosite_entry-rrc Cshz td|d}Wnty#}z |jdkrtd|dd}~ww|jdkr2td|dd|S) ahGet 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 zhttps://prosite.expasy.org/.txtz#Failed to find entry '%s' on ExPASyNzhttps://www.expasy.org/zFailed to find entry 'z ' on ExPASy)rrcode ValueErrorurl)r r handle exceptionr r r get_prosite_rawBs  rc CsNz td|d}W|Sty&}z|jdvr!td|ddd}~ww)aGet 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' zhttp://www.uniprot.org/uniprot/r)irz Failed to find SwissProt entry ''N)rrrr)r rrr r r get_sprot_rawes rcCs"t|}tj|dd}|j|_|S)z?Open URL and convert to text assuming UTF-8 encoding (PRIVATE).zUTF-8)encoding)rio TextIOWrapperr)rr text_handler r r rsr)r)r)N) __doc__r urllib.errorrurllib.requestrrrrrrr r r r s    #