Bio.ExPASy package¶
Submodules¶
Module contents¶
Code to access resources at ExPASy over the WWW.
- 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.
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Bio.ExPASy.
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 >>> in_handle = ExPASy.get_prodoc_entry('PDOC00001') >>> html = in_handle.read() >>> in_handle.close() ... >>> with open("myprodocrecord.html", "w") as out_handle: ... # Python2/3 docstring workaround: Revise for 'Python 3 only' ... _ = out_handle.write(html) ...
For a non-existing key XXX, ExPASy returns an HTML-formatted page containing this text: ‘There is currently no PROSITE entry for’
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Bio.ExPASy.
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 >>> in_handle = ExPASy.get_prosite_entry('PS00001') >>> html = in_handle.read() >>> in_handle.close() ... >>> with open("myprositerecord.html", "w") as out_handle: ... # Python 2/3 docstring workaround: Revise for 'Python 3 only' ... _ = out_handle.write(html) ...
For a non-existing key XXX, ExPASy returns an HTML-formatted page containing this text: ‘There is currently no PROSITE entry for’
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Bio.ExPASy.
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 >>> handle = ExPASy.get_prosite_raw('PS00001') >>> record = Prosite.read(handle) >>> handle.close() >>> print(record.accession) PS00001
For a non-existing key, ExPASy returns an error:
>>> # Python 2/3 docstring workaround: Revise for 'Python 3 only' >>> try: ... handle = ExPASy.get_prosite_raw("does_not_exist") ... except Exception as e: ... print('HTTPError: %s' %e) HTTPError: ... Error 404: Not Found
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Bio.ExPASy.
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 >>> handle = ExPASy.get_sprot_raw("O23729") >>> record = SwissProt.read(handle) >>> handle.close() >>> print(record.entry_name) CHS3_BROFI
For a non-existing identifier, UniProt returns an error:
>>> # Python2/3 docstring workaround: Revise for 'Python 3 only' >>> try: ... ExPASy.get_sprot_raw("DOES_NOT_EXIST") ... except Exception as e: ... print('HTTPError: %s' %e) HTTPError: ... Error 404: