Closed widdowquinn closed 1 year ago
@widdowquinn Uniprot has changed its API recently. I have updated bioservices but not the documentation.
It is now updated on bioservices.readthedocs.io
Unfortunately, the uniprot API has changed a lot for the best (json support for instance). However, this means that previous code will need to be changed accordingly. I tried to keep track of the changed to a minimum level.
as for your example, indeed taxonomy should be taxonomy_id and organism should be organism_id
@widdowquinn I have now fixed the documentation that should be updated
While investigating an error in
ncfp
I came across a problem stemming frombioservices
. Following the "Quick Example" inREADME.md
, I prepared a short Python script calledtest_bioservices.py
, containing:Executing this gives the error:
Fixing the
frmt
argument (tsv
in place oftab
) gives the following error:matching the errors I was seeing in
ncfp
.Version information is below:
I think the
taxonomy
field in the example query needs to be modified totaxonomy_id
, as per https://www.uniprot.org/help/query-fields:gives