Module: ncbi.datasets.openapi.api.prokaryote_api

NCBI Datasets API

Module: ncbi.datasets.openapi.api.prokaryote_api

NCBI Datasets API

### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets API is still in alpha, and we’re updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated bag](https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/datasets/docs/rehydrate/), and retrieve the individual data files at a later time. # noqa: E501

The version of the OpenAPI document: v1 Generated by: https://openapi-generator.tech

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

Bases: object

NOTE: This class is auto generated by OpenAPI Generator Ref: https://openapi-generator.tech

Do not edit the class manually.

download_prokaryote_gene_package(accessions, **kwargs)

Get a prokaryote gene dataset by RefSeq protein accession # noqa: E501

Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession. # noqa: E501 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

accessions ([str]) – WP prokaryote protein accession

Keyword Arguments
  • include_annotation_type ([V1Fasta]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.. [optional]

  • gene_flank_config_length (int) – [optional]

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

  • filename (str) – Output file name.. [optional] if omitted the server will use the default value of “ncbi_dataset.zip”

  • _return_http_data_only (bool) – response data without head status code and headers. Default is True.

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

  • _request_timeout (int/float/tuple) – 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. Default is None.

  • _check_input_type (bool) – specifies if type checking should be done one the data sent to the server. Default is True.

  • _check_return_type (bool) – specifies if type checking should be done one the data received from the server. Default is True.

  • _host_index (int/None) – specifies the index of the server that we want to use. Default is read from the configuration.

  • async_req (bool) – execute request asynchronously

Returns

file_type

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

download_prokaryote_gene_package_post(v1_prokaryote_gene_request, **kwargs)

Get a prokaryote gene dataset by RefSeq protein accession by POST # noqa: E501

Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession by POST. # noqa: E501 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(v1_prokaryote_gene_request, async_req=True)
>>> result = thread.get()
Parameters

v1_prokaryote_gene_request (V1ProkaryoteGeneRequest) –

Keyword Arguments
  • filename (str) – Output file name.. [optional] if omitted the server will use the default value of “ncbi_dataset.zip”

  • _return_http_data_only (bool) – response data without head status code and headers. Default is True.

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

  • _request_timeout (int/float/tuple) – 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. Default is None.

  • _check_input_type (bool) – specifies if type checking should be done one the data sent to the server. Default is True.

  • _check_return_type (bool) – specifies if type checking should be done one the data received from the server. Default is True.

  • _host_index (int/None) – specifies the index of the server that we want to use. Default is read from the configuration.

  • async_req (bool) – execute request asynchronously

Returns

file_type

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

Generated October 18, 2021