Actionable Mutation Annotation

actionable_mutations_oncokb¶

Short description¶

Annotates mutation data using the OncoKB API to add actionable mutation information and therapeutic implications.

Signature¶

def actionable_mutations_oncokb(self, token: str, batch_size: int = 5000, timeout: int = 30, max_retries: int = 3, retry_backoff: float = 1.0) -> pd.DataFrame:

Parameters¶

Parameter	Type	Required	Description
`token`	`str`	Yes	OncoKB API authentication token required for accessing the OncoKB service.
`batch_size`	`int`	No	Maximum number of variants to send in a single API request (default: 5000).
`timeout`	`int`	No	Timeout for API requests in seconds (default: 30).
`max_retries`	`int`	No	Maximum number of retries for failed API requests (default: 3).
`retry_backoff`	`float`	No	Backoff factor for retries, controls delay between retry attempts (default: 1.0).

Return value¶

Returns a pd.DataFrame containing the original self.data DataFrame with OncoKB annotations added as columns. The annotations include therapeutic implications and actionable mutation information.

Exceptions¶

List only those the user should handle:

ValueError: if the DataFrame doesn't contain the necessary data for export (missing required columns like CHROM, POS, REF, ALT) or if the reference genome is invalid.
requests.exceptions.RequestException: if there's an error with the API request that can't be resolved with retries.

Minimal usage example¶

>>> # Assuming you have a valid OncoKB API token
>>> token = "your_oncokb_api_token"
>>> annotated_data = pymutation_obj.actionable_mutations_oncokb(token)
>>> print(annotated_data.columns)