rotifer.db.uniprot.webapi#

Query UniProt’s REST web services.

rotifer.db.uniprot.webapi.idmapping implements the identifier mapping workflow: submit a batch of accessions, poll until the job finishes and download the results.

Cursors#

SequenceCursor

Entries with their annotation, as Bio.SeqRecord objects.

FastaCursor

The same entries as plain sequences.

SearchCursor

Any resource, as a dataframe, by identifier or by query.

ProteomeCursor

Proteome descriptions.

TaxonomyCursor

Taxonomy records.

MappingCursor

Identifier translation, in either direction, read off the cross-references an entry carries.

Extra API parameters#

UniProt’s API accepts many options these classes know nothing about. Any keyword a cursor does not recognise is passed straight through as a query parameter, so they all remain available:

>>> fc = webapi.FastaCursor(includeIsoform=True)
>>> sc = webapi.SearchCursor(database='uniprotkb',
...                          fields='accession,id,length')

See Also#

rotifer.db.uniprot : delegators combining this backend with the others rotifer.db.ncbi : the equivalent cursors for NCBI