Bio.ExPASy package

Submodules

Module contents

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.

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
>>> 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’

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
>>> 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’

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
>>> 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
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
>>> 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'