Module: ncbi.datasets.openapi.api.taxonomy_api

NCBI Datasets API

Module: ncbi.datasets.openapi.api.taxonomy_api

NCBI Datasets API

### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 1 API is considred stable and will not be subject to breaking changes. 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/v1/how-tos/genomes/large-download/), 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.taxonomy_api.TaxonomyApi(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.

tax_name_query(taxon_query, **kwargs)

Get a list of taxonomy names and IDs given a partial taxonomic name # noqa: E501

This endpoint retrieves a list of taxonomy names and IDs given a partial taxonomic name of any rank. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.tax_name_query(taxon_query, async_req=True)
>>> result = thread.get()
Parameters

taxon_query (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank

Keyword Arguments
  • tax_rank_filter (V1OrganismQueryRequestTaxRankFilter) – Set the scope of searched tax ranks. [optional]

  • _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

V1SciNameAndIds

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

taxonomy_filtered_subtree(taxons, **kwargs)

Use taxonomic identifiers to get a filtered taxonomic subtree # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_filtered_subtree(taxons, async_req=True)
>>> result = thread.get()
Parameters

taxons ([str]) –

Keyword Arguments
  • specified_limit (bool) – Limit to specified species. [optional]

  • rank_limits ([V1OrganismRankType]) – Limit to the provided ranks. If empty, accept any rank.. [optional]

  • _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

V1TaxonomyFilteredSubtreeResponse

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

taxonomy_filtered_subtree_post(v1_taxonomy_filtered_subtree_request, **kwargs)

Use taxonomic identifiers to get a filtered taxonomic subtree by post # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_filtered_subtree_post(v1_taxonomy_filtered_subtree_request, async_req=True)
>>> result = thread.get()
Parameters

v1_taxonomy_filtered_subtree_request (V1TaxonomyFilteredSubtreeRequest) –

Keyword Arguments
  • _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

V1TaxonomyFilteredSubtreeResponse

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

taxonomy_metadata(taxons, **kwargs)

Use taxonomic identifiers to get taxonomic metadata # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_metadata(taxons, async_req=True)
>>> result = thread.get()
Parameters

taxons ([str]) –

Keyword Arguments
  • returned_content (V1TaxonomyMetadataRequestContentType) – Return either tax-ids alone, or entire taxononmy-metadata records. [optional]

  • _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

V1TaxonomyMetadataResponse

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

taxonomy_metadata_post(v1_taxonomy_metadata_request, **kwargs)

Use taxonomic identifiers to get taxonomic metadata by post # noqa: E501

Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.taxonomy_metadata_post(v1_taxonomy_metadata_request, async_req=True)
>>> result = thread.get()
Parameters

v1_taxonomy_metadata_request (V1TaxonomyMetadataRequest) –

Keyword Arguments
  • _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

V1TaxonomyMetadataResponse

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

Generated December 6, 2022