chemicalchecker.database.uniprotkb.UniprotKB

class UniprotKB(version, host=None, user=None, pwd=None, port=None)[source]

Bases: object

This class provides an interface to querying the internal database UniprotKB

Methods

`close_conn`
`get_protein`	Returns the specified protein record
`get_proteins`	Returns the records for all specified proteins.
`get_reference_proteome`	Returns the set of Uniprot ACs belonging to the reference proteome for the organism corresponding to the tax_id.
`map_names_to_uniprot_acs`	Maps names to Uniprot AC (like ORF names, for ex.).
`map_protein_to_uniref100_representative`	Returns the Uniprot ACs representative of the Uniref100 cluster to which uniprot_ac belongs.
`map_secondary_to_primary`	Maps a secondary Uniprot AC to a primary one.
`map_xrefs_to_uniprot_acs`	Maps external IDs to Uniprot AC.
`pick_reference`	Among a set of ambiguously mapped uniprot ACs that, supposedly, refer to the same entity, this function picks the "best", defined as the one corresponding to one of the organism tax ids that is:

Attributes

`DEFAULT_HOST`
`DEFAULT_PWD`
`DEFAULT_USER`
`SRC_DB_EMBL`
`SRC_DB_ENSEMBL`
`SRC_DB_FLYBASE`
`SRC_DB_GENEID`
`SRC_DB_GI`
`SRC_DB_HGNC`
`SRC_DB_REFSEQ`
`SRC_DB_SGD`
`SRC_DB_WORMBASE`
`UNIPROTKB_TABLES`

get_protein(uniprot_ac, limit_to_fields=None)[source]: Returns the specified protein record

get_proteins(uniprot_acs, limit_to_fields=None)[source]: Returns the records for all specified proteins.

get_reference_proteome(tax_id, only_reviewed=False)[source]: Returns the set of Uniprot ACs belonging to the reference proteome for the organism corresponding to the tax_id.

map_names_to_uniprot_acs(names, filter_sources=None, filter_taxids=None)[source]: Maps names to Uniprot AC (like ORF names, for ex.).

map_protein_to_uniref100_representative(uniprot_ac)[source]: Returns the Uniprot ACs representative of the Uniref100 cluster to which uniprot_ac belongs.

map_secondary_to_primary(uniprot_ac)[source]: Maps a secondary Uniprot AC to a primary one.

map_xrefs_to_uniprot_acs(ids, filter_dbs=None)[source]: Maps external IDs to Uniprot AC.

pick_reference(uniprot_acs, organism_tax_ids=None, only_one=True)[source]

Among a set of ambiguously mapped uniprot ACs that, supposedly, refer to the same entity, this function picks the “best”, defined as the one corresponding to one of the organism tax ids that is:

the longest among the ones that are reviewed and assigned to the Complete and Reference proteome

if not, the longest among the ones that are reviewed and assigned to the Reference proteome

if not, the longest among the ones that are reviewed and assigned to the Complete proteome

if not, the longest among the ones that are assigned to the Complete and Reference proteome

if not, the longest among the ones that are assigned to the Reference proteome

if not, the longest among the ones that are assigned to the Complete proteome

if not, the longest among the ones that are reviewed

if not, the longest

If only_one is set to false, instead of returning the “longest among…” it returns the entire list of proteins satisfying each condition.