mkt.databases.ncbi.ProteinNCBI

class mkt.databases.ncbi.ProteinNCBI(accession: str, url: str = 'https://api.ncbi.nlm.nih.gov/datasets/v2/protein/accession/<ACC>/download?', annotation: str | None = 'FASTA_PROTEIN', headers: str = "{'Accept': 'application/zip'}", str_fasta: str | None = None, list_headers: list[str | None] = <factory>, list_seq: list[str | None] = <factory>)

Bases: RESTAPIClient

Class to interact with query NCBI Protein API; only FASTA download supported.

__init__(*args: Any, **kwargs: Any) → None

Methods

__eq__(other)	Return self==value.
__post_init__()
_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.
create_query_url()	Create URL for NCBI Protein API query.
process_fasta(str_fasta)	Process downloaded FASTA file or string into headers and sequences.
query_api()

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
__pydantic_config__
annotation	FASTA_UNSPECIFIED ┃ FASTA_GENE ┃ FASTA_RNA ┃ FASTA_PROTEIN ┃ FASTA_GENE_FLANK ┃ FASTA_CDS ┃ FASTA_5P_UTR ┃ FASTA_3P_UTR.
from_cache	Whether the most recent response was served from requests-cache.
headers	Header for the API request.
query_datetime	UTC datetime the underlying network query was made (cache creation time if served from cache).
str_fasta	FASTA string downloaded from NCBI.
url	URL for the NCBI Protein API.
accession	Accession ID for the protein.
list_headers	List of FASTA headers.
list_seq	List of FASTA sequences.

accession: str

Accession ID for the protein.

annotation: str | None = 'FASTA_PROTEIN'

FASTA_UNSPECIFIED ┃ FASTA_GENE ┃ FASTA_RNA ┃ FASTA_PROTEIN ┃ FASTA_GENE_FLANK ┃ FASTA_CDS ┃ FASTA_5P_UTR ┃ FASTA_3P_UTR.

Type:

Annotation type to include in the download

create_query_url()

Create URL for NCBI Protein API query.

headers: str = "{'Accept': 'application/zip'}"

Header for the API request.

list_headers: list[str | None]

List of FASTA headers.

list_seq: list[str | None]

List of FASTA sequences.

static process_fasta(str_fasta: str) → tuple[list[str], list[str]]

Process downloaded FASTA file or string into headers and sequences.

Parameters:

str_fastastr

FASTA string to process.

Returns:

tuple[list[str], list[str]]

Lists of FASTA headers and sequences.

query_api() → dict

str_fasta: str | None = None

FASTA string downloaded from NCBI.

url: str = 'https://api.ncbi.nlm.nih.gov/datasets/v2/protein/accession/<ACC>/download?'

URL for the NCBI Protein API.