mkt.databases.oncokb.OncoKBProteinChange

class mkt.databases.oncokb.OncoKBProteinChange(url: str = 'https://www.oncokb.org/api/v1', header: dict = <factory>, gene_name: str | None = None, alteration: str | None = None, dict_highest_level: dict[str, int] = <factory>, list_treatment: list[str] = <factory>, oncogenic: str | None = None, vus: bool | None = None, known_effect: str | None = None, verbose: bool = True)

Bases: OncoKB

OncoKB API client for protein changes.

__init__(url: str = 'https://www.oncokb.org/api/v1', header: dict = <factory>, gene_name: str | None = None, alteration: str | None = None, dict_highest_level: dict[str, int] = <factory>, list_treatment: list[str] = <factory>, oncogenic: str | None = None, vus: bool | None = None, known_effect: str | None = None, verbose: bool = True) → None

Methods

__eq__(other)	Return self==value.
__init__([url, header, gene_name, ...])
__post_init__()	Initialize the OncoKBProteinChange client.
_stamp_from_response(res)	Record query datetime + cache provenance from a requests-cache response.
_stamp_now()	Record current UTC datetime; cache provenance unknown.
annotate_highest_level()	Annotate the highest level of evidence for the protein change.
check_response(res)	Check the response status code for errors.
extract_level_as_int(str_in)	Extract the level from a string and convert it to an integer.
get_treatments()	Get the list of treatments associated with the alteration.
has_json()	Get the JSON response from the OncoKB API query.
maybe_get_token()	Get API token, if available.
query_api()	Query the OncoKB API for a given URL.
set_api_key()	Set API token for REST API.
update_url()	Update the URL for the OncoKB API query based on the UniProt ID.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
_json
alteration	Alteration type (e.g., V600E if BRAF is gene).
from_cache	Whether the most recent response was served from requests-cache.
gene_name	Gene associated with the protein change.
known_effect	Effect of the mutation on the protein (e.g., missense, nonsense).
oncogenic	Oncogenic status of the alteration.
query_datetime	UTC datetime the underlying network query was made (cache creation time if served from cache).
url	Base URL for the OncoKB API.
url_query	URL to update for specific queries.
verbose	Whether to log warnings for missing data.
vus	Whether the alteration is a Variant of Uncertain Significance (VUS).
dict_highest_level	Dictionary to store the highest level of evidence for each alteration.
list_treatment	List of treatments associated with the alteration.
header	OncoKB API token, if available.

__init__(url: str = 'https://www.oncokb.org/api/v1', header: dict = <factory>, gene_name: str | None = None, alteration: str | None = None, dict_highest_level: dict[str, int] = <factory>, list_treatment: list[str] = <factory>, oncogenic: str | None = None, vus: bool | None = None, known_effect: str | None = None, verbose: bool = True) → None

alteration: str | None = None

Alteration type (e.g., V600E if BRAF is gene).

annotate_highest_level()

Annotate the highest level of evidence for the protein change.

dict_highest_level: dict[str, int]

Dictionary to store the highest level of evidence for each alteration.

gene_name: str | None = None

Gene associated with the protein change.

get_treatments()

Get the list of treatments associated with the alteration.

header: dict

OncoKB API token, if available.

known_effect: str | None = None

Effect of the mutation on the protein (e.g., missense, nonsense).

list_treatment: list[str]

List of treatments associated with the alteration.

oncogenic: str | None = None

Oncogenic status of the alteration.

update_url()

Update the URL for the OncoKB API query based on the UniProt ID.

verbose: bool = True

Whether to log warnings for missing data.

vus: bool | None = None

Whether the alteration is a Variant of Uncertain Significance (VUS).