mkt.databases.uniprot.UniProtFASTA

class mkt.databases.uniprot.UniProtFASTA(uniprot_id: str, url: str = 'https://rest.uniprot.org/uniprotkb', url_fasta: str | None = None, _header: str | None = None, _sequence: str | None = None)

Bases: UniProt, RESTAPIClient

Class to interact UniProt API for FASTA download.

__init__(uniprot_id: str, url: str = 'https://rest.uniprot.org/uniprotkb', url_fasta: str | None = None, _header: str | None = None, _sequence: str | None = None) → None

Methods

__eq__(other)	Return self==value.
__init__(uniprot_id[, url, url_fasta, ...])
__post_init__()
_convert_fasta2seq(str_fasta)	Convert FASTA sequence to string sequence (i.e., remove header line breaks).
_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.
query_api([bool_seq])	Get FASTA sequence for UniProt ID.
set_url()	Set URL for UniProt API; UniProtKB if SwissProt or Unisave if TrEMBL.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
_header	FASTA header.
_sequence	FASTA sequence.
from_cache	Whether the most recent response was served from requests-cache.
query_datetime	UTC datetime the underlying network query was made (cache creation time if served from cache).
url	URL for the UniProt API.
url_fasta	URL for the UniProt FASTA API including UniProt ID.
uniprot_id	UniProt ID.

__init__(uniprot_id: str, url: str = 'https://rest.uniprot.org/uniprotkb', url_fasta: str | None = None, _header: str | None = None, _sequence: str | None = None) → None

static _convert_fasta2seq(str_fasta) → tuple[str, str]

Convert FASTA sequence to string sequence (i.e., remove header line breaks).

Parameters:

str_fasta (str) – FASTA string (including header and line breaks)

Returns:

header, seq – FASTA header and sequence strings (excluding line breaks)

Return type:

tuple[str, str]

query_api(bool_seq: bool = True) → str | None

Get FASTA sequence for UniProt ID.

Parameters:

bool_seq (bool) – If True, return sequence string only (i.e., no header or line breaks); otherwise return full FASTA string

Returns:

FASTA sequences for UniProt ID; None if request fails

Return type:

str | None

set_url()

Set URL for UniProt API; UniProtKB if SwissProt or Unisave if TrEMBL.

uniprot_id: str

UniProt ID.

url_fasta: str | None = None

URL for the UniProt FASTA API including UniProt ID.