mkt.databases.hgnc.HGNC

class mkt.databases.hgnc.HGNC(input_symbol_or_id: str, input_is_hgnc_symbol: bool = True, url: str = 'https://rest.genenames.org')

Bases: RESTAPIClient

Class to interact with the HGNC API.

__init__(input_symbol_or_id: str, input_is_hgnc_symbol: bool = True, url: str = 'https://rest.genenames.org') → None

Methods

__eq__(other)	Return self==value.
__init__(input_symbol_or_id[, ...])
__post_init__()	Post-initialization to set HGNC gene symbol or Ensembl gene ID.
_extract_list_from_hgnc_response_docs(...)	Extract a list of values from the response documents of an HGNC REST API request.
_generate_key_set_hgnc_response_docs(res_input)	Generate a set of keys present in the response documents of an HGNC REST API request.
_stamp_from_response(res)	Record query datetime + cache provenance from a requests-cache response.
_stamp_now()	Record current UTC datetime; cache provenance unknown.
check_response(res)	Check the response status code for errors.
maybe_get_info_from_hgnc_fetch([...])	Get gene information for a given HGNC gene name from gene symbol report using HGNC REST API.
maybe_get_symbol_from_hgnc_search([...])	Get gene name from HGNC REST API using either a gene symbol or an Ensembl gene ID.
query_api(**kwargs)	Default HGNC query: forwards to maybe_get_symbol_from_hgnc_search.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
from_cache	Whether the most recent response was served from requests-cache.
input_is_hgnc_symbol	If True, input_symbol_or_id is a gene symbol, otherwise it is an Ensembl gene ID.
query_datetime	UTC datetime the underlying network query was made (cache creation time if served from cache).
url	HGNC API URL.
input_symbol_or_id	Gene symbol or Ensembl gene ID.

__init__(input_symbol_or_id: str, input_is_hgnc_symbol: bool = True, url: str = 'https://rest.genenames.org') → None

static _extract_list_from_hgnc_response_docs(res_input: Response, str_to_extract: str) → list[str]

Extract a list of values from the response documents of an HGNC REST API request.

Parameters:

• res_input (requests.models.Response) – Response object from an HGNC REST API request

• str_to_extract (str) – Key to extract from the response documents

Returns:

List of values extracted from the response documents

Return type:

list[str]

static _generate_key_set_hgnc_response_docs(res_input: Response) → set[str]

Generate a set of keys present in the response documents of an HGNC REST API request.

Parameters:

res_input (requests.models.Response) – Response object from an HGNC REST API request

Returns:

Set of keys present in the response documents

Return type:

set[str]

input_is_hgnc_symbol: bool = True

If True, input_symbol_or_id is a gene symbol, otherwise it is an Ensembl gene ID.

input_symbol_or_id: str

Gene symbol or Ensembl gene ID.

maybe_get_info_from_hgnc_fetch(list_to_extract: list[str] | None = None, bool_verbose: bool = False) → dict | None

Get gene information for a given HGNC gene name from gene symbol report using HGNC REST API.

Parameters:

• hgnc_gene_symbol (str) – HGNC gene symbol

• list_to_extract (list[str] | None) – List of fields to extract from the response; if None, defaults to [“locus_type”]

• bool_verbose (bool, optional) – Whether to log verbose messages, by default False.

Returns:

Dictionary of gene information; empty list if no match and None if request fails or field not found

Return type:

dict | None

Notes

The list of extractable fields can be found at https://www.genenames.org/help/rest/ under “storedFields” in the JSON or XML outputs.

maybe_get_symbol_from_hgnc_search(custom_field: str | None = None, custom_term: str | None = None, bool_verbose: bool = False) → list[str] | None

Get gene name from HGNC REST API using either a gene symbol or an Ensembl gene ID.

Parameters:

• custom_field (str | None) – Optional: custom field to search for in the HGNC REST API; otherwise defaults to “symbol” or “ensembl_gene_id” See https://www.genenames.org/help/rest/ under “searchableFields” for options

• custom_term (str | None) – Optional: custom term to search for in the HGNC REST API

• bool_verbose (bool, optional) – Whether to log verbose messages, by default False.

Returns:

List of gene names that match input_symbol_or_id; empty list if no match and None if request fails

Return type:

list[str] | None

query_api(**kwargs) → list[str] | None

Default HGNC query: forwards to maybe_get_symbol_from_hgnc_search.

Parameters:

**kwargs

Forwarded to maybe_get_symbol_from_hgnc_search.

Returns:

list[str] | None

Result of the search; see maybe_get_symbol_from_hgnc_search for details.

url: str = 'https://rest.genenames.org'

HGNC API URL.