mkt.databases.pfam

Pfam API client and helper for locating kinase-domain boundaries.

Provides Pfam, a REST client for Pfam domain annotations, and find_pfam_domain() to identify kinase-domain boundaries for a sequence.

Functions

find_pfam_domain(input_id, input_position, ...)

Find Pfam domain for a given HGNC symbol and position

Classes

Pfam(uniprot_id[, url])

Class to interact with the Pfam API.
class mkt.databases.pfam.Pfam(uniprot_id: str, url: str = 'https://www.ebi.ac.uk/interpro/api/entry/pfam/protein/UniProt/')[source]

Bases: RESTAPIClient

Class to interact with the Pfam API.

__init__(uniprot_id: str, url: str = 'https://www.ebi.ac.uk/interpro/api/entry/pfam/protein/UniProt/') → None
query_api()[source]

Queries Pfam API for UniProt ID as DataFrame object.

Returns:

DataFrame with Pfam domain information if request is successful, None if response is empty or request fails

Return type:

pd.DataFrame | str | None

uniprot_id: str

UniProt ID to query Pfam API.

url: str = 'https://www.ebi.ac.uk/interpro/api/entry/pfam/protein/UniProt/'

Pfam API URL.

mkt.databases.pfam.find_pfam_domain(input_id: str, input_position: int, df_ref: DataFrame, col_ref_id: str, col_ref_start: str | None = None, col_ref_end: str | None = None, col_ref_domain: str | None = None) → str | None[source]

Find Pfam domain for a given HGNC symbol and position

Parameters:

  • input_id (str) – Input ID that matches

  • input_position (int) – Codon position in UniProt canonical sequence

  • df_ref (pd.DataFrame) – DataFrame with Pfam domain information

  • col_ref_id (str) – Column that contains the IDs to match to in the df_ref dataframe

  • col_ref_start (None | str) – Column containing the domain start position; if None defaults to “start” (Pfam API default)

  • col_ref_end (None | str) – Column containing the domain end position; if None defaults to “end” (Pfam API default)

  • col_ref_domain (None | str) – Column containing the domain name; if None defaults to “name” (Pfam API default)

Returns:

Pfam domain if found, None if not found

Return type:

str | None