Module: ncbi.datasets.openapi.api.prokaryote_api

Python API: ncbi.datasets.openapi.api.prokaryote_api

Module: ncbi.datasets.openapi.api.prokaryote_api

Python API: ncbi.datasets.openapi.api.prokaryote_api
class ncbi.datasets.openapi.api.prokaryote_api.ProkaryoteApi(api_client=None)

Bases: object

download_prokaryote_gene_package(accessions, **kwargs)

Get a prokaryote gene dataset by RefSeq protein accession

Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.download_prokaryote_gene_package(accessions, async_req=True)
result = thread.get()
Parameters

  • bool (async_req) – execute request asynchronously

  • accessions (list[str]) – WP prokaryote protein accession (required)

  • include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

  • gene_flank_config_length (int) –

  • taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree.

  • filename (str) – Output file name.

  • _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts.

Returns

file If the method is called asynchronously, returns the request thread.

download_prokaryote_gene_package_post(body, **kwargs)

Get a prokaryote gene dataset by RefSeq protein accession by POST

Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession by POST. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.download_prokaryote_gene_package_post(body, async_req=True)
result = thread.get()
Parameters

  • bool (async_req) – execute request asynchronously

  • body (V1alpha1ProkaryoteGeneRequest) – (required)

  • filename (str) – Output file name.

  • _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts.

Returns

file If the method is called asynchronously, returns the request thread.

download_prokaryote_gene_package_post_with_http_info(body, **kwargs)

Get a prokaryote gene dataset by RefSeq protein accession by POST

Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession by POST. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.download_prokaryote_gene_package_post_with_http_info(body, async_req=True)
result = thread.get()
Parameters

  • bool (async_req) – execute request asynchronously

  • body (V1alpha1ProkaryoteGeneRequest) – (required)

  • filename (str) – Output file name.

  • _return_http_data_only – response data without head status code and headers

  • _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts.

Returns

tuple(file, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.

download_prokaryote_gene_package_with_http_info(accessions, **kwargs)

Get a prokaryote gene dataset by RefSeq protein accession

Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.download_prokaryote_gene_package_with_http_info(accessions, async_req=True)
result = thread.get()
Parameters

  • bool (async_req) – execute request asynchronously

  • accessions (list[str]) – WP prokaryote protein accession (required)

  • include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

  • gene_flank_config_length (int) –

  • taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree.

  • filename (str) – Output file name.

  • _return_http_data_only – response data without head status code and headers

  • _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

  • _request_timeout – timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts.

Returns

tuple(file, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.

Generated April 23, 2021