mkt.databases.uniprot.UniProtRefSeqProteinGET

class mkt.databases.uniprot.UniProtRefSeqProteinGET(identifier: str, term_in: str | None, term_out: str | None, url_base: str, headers: str | None = None, polling_interval: int = 5, jobId: str | None = None)

Bases: UniProtGET

Class to interact with UniProt API bulk download for list of RefSeqProtein identifiers via GET.

__init__(identifier: str, term_in: str | None, term_out: str | None, url_base: str, headers: str | None = None, polling_interval: int = 5, jobId: str | None = None) → None

Methods

__eq__(other)	Return self==value.
__init__(identifier, term_in, term_out, url_base)
__post_init__()
check_if_job_ready()	Check if the job is ready and add json if so.
check_response(res)	Check the response status code for errors.
concatenate_json_batches()	Concatenate json from batches and return as dictionary.
create_query_url()	Create URL for UniProt API query.
get_batch()	Get batches of json from UniProt API.
get_next_link(headers)	Get next link from headers.
maybe_get_gene_names()	Get list of gene names from UniProt ID and add as list_gene_names attr.
process_identifier()	Process identifier string input to standardize, overwrite, and add as list.
query_api()	Get response from API which tries to save as json in instance; otherwise saves as text.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
headers	Headers for API (use ast.as_literal to convert to dict).
jobId	Job ID for bulk download; applies to UniProt bulk downloading.
polling_interval	Interval in seconds to poll API for job status.
identifier	Identifier or comma delimited list of identifiers from which to map.
term_in	Term on which from which to map.
term_out	Term on which to which to map, if needed.
url_base	URL base for API.

__init__(identifier: str, term_in: str | None, term_out: str | None, url_base: str, headers: str | None = None, polling_interval: int = 5, jobId: str | None = None) → None

check_if_job_ready()

Check if the job is ready and add json if so.

concatenate_json_batches()

Concatenate json from batches and return as dictionary.

maybe_get_gene_names()

Get list of gene names from UniProt ID and add as list_gene_names attr.