Module: ncbi.datasets.openapi.api.gene_api

NCBI Datasets API

Module: ncbi.datasets.openapi.api.gene_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.gene_api.GeneApi(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_gene_package(gene_ids, **kwargs)

Get a gene dataset by gene ID # noqa: E501

Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata by gene ID. # 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_gene_package(gene_ids, async_req=True)
>>> result = thread.get()
Parameters

gene_ids ([int]) – NCBI gene ids

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

  • fasta_filter ([str]) – Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [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_gene_package_post(v1_gene_dataset_request, **kwargs)

Get a gene dataset by POST # noqa: E501

Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata 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_gene_package_post(v1_gene_dataset_request, async_req=True)
>>> result = thread.get()
Parameters

v1_gene_dataset_request (V1GeneDatasetRequest) –

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.

gene_download_summary_by_accession(accessions, **kwargs)

Get gene download summary by RefSeq Accession # noqa: E501

Get gene download summary by RefSeq Accession in a JSON output 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.gene_download_summary_by_accession(accessions, async_req=True)
>>> result = thread.get()
Parameters

accessions ([str]) – RNA or Protein accessions.

Keyword Arguments
  • fasta_filter ([str]) – Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [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

V1DownloadSummary

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

gene_download_summary_by_id(gene_ids, **kwargs)

Get gene download summary by GeneID # noqa: E501

Get a download summary by GeneID in a JSON output 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.gene_download_summary_by_id(gene_ids, async_req=True)
>>> result = thread.get()
Parameters

gene_ids ([int]) – NCBI gene ids

Keyword Arguments
  • fasta_filter ([str]) – Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [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

V1DownloadSummary

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

gene_download_summary_by_post(v1_gene_dataset_request, **kwargs)

Get gene download summary # noqa: E501

Get gene download summary in a JSON output 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.gene_download_summary_by_post(v1_gene_dataset_request, async_req=True)
>>> result = thread.get()
Parameters

v1_gene_dataset_request (V1GeneDatasetRequest) –

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

V1DownloadSummary

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

gene_download_summary_by_tax_and_symbol(symbols, taxon, **kwargs)

Get gene download summary by gene symbol # noqa: E501

Get gene download summary by gene symbol in a JSON output 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.gene_download_summary_by_tax_and_symbol(symbols, taxon, async_req=True)
>>> result = thread.get()
Parameters
  • symbols ([str]) – Gene symbol

  • taxon (str) – Taxon for provided gene symbol

Keyword Arguments
  • fasta_filter ([str]) – Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [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

V1DownloadSummary

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

gene_metadata_by_accession(accessions, **kwargs)

Get gene metadata by RefSeq Accession # noqa: E501

Get detailed gene metadata by RefSeq Accession in a JSON output 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.gene_metadata_by_accession(accessions, async_req=True)
>>> result = thread.get()
Parameters

accessions ([str]) – RNA or Protein accessions.

Keyword Arguments
  • returned_content (V1GeneDatasetRequestContentType) – Return either gene-ids, or entire gene metadata. [optional]

  • sort_schema_field (V1GeneDatasetRequestSortField) – Select a field to sort on.. [optional]

  • sort_schema_direction (V1SortDirection) – Select a direction for the sort.. [optional]

  • limit (str) – Limit the number of returned results (“all”, “none”, otherwise an integer value). [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

V1GeneMetadata

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

gene_metadata_by_id(gene_ids, **kwargs)

Get gene metadata by GeneID # noqa: E501

Get detailed gene metadata by GeneID in a JSON output 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.gene_metadata_by_id(gene_ids, async_req=True)
>>> result = thread.get()
Parameters

gene_ids ([int]) – NCBI gene ids

Keyword Arguments
  • returned_content (V1GeneDatasetRequestContentType) – Return either gene-ids, or entire gene metadata. [optional]

  • sort_schema_field (V1GeneDatasetRequestSortField) – Select a field to sort on.. [optional]

  • sort_schema_direction (V1SortDirection) – Select a direction for the sort.. [optional]

  • limit (str) – Limit the number of returned results (“all”, “none”, otherwise an integer value). [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

V1GeneMetadata

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

gene_metadata_by_post(v1_gene_dataset_request, **kwargs)

Get gene metadata as JSON # noqa: E501

Get detailed gene metadata in a JSON output 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.gene_metadata_by_post(v1_gene_dataset_request, async_req=True)
>>> result = thread.get()
Parameters

v1_gene_dataset_request (V1GeneDatasetRequest) –

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

V1GeneMetadata

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

gene_metadata_by_tax_and_symbol(symbols, taxon, **kwargs)

Get gene metadata by gene symbol # noqa: E501

Get detailed gene metadata by gene symbol in a JSON output 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.gene_metadata_by_tax_and_symbol(symbols, taxon, async_req=True)
>>> result = thread.get()
Parameters
  • symbols ([str]) – Gene symbol

  • taxon (str) – Taxon for provided gene symbol

Keyword Arguments
  • accessions ([str]) – RNA or Protein accessions.. [optional]

  • returned_content (V1GeneDatasetRequestContentType) – Return either gene-ids, or entire gene metadata. [optional]

  • sort_schema_field (V1GeneDatasetRequestSortField) – Select a field to sort on.. [optional]

  • sort_schema_direction (V1SortDirection) – Select a direction for the sort.. [optional]

  • limit (str) – Limit the number of returned results (“all”, “none”, otherwise an integer value). [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

V1GeneMetadata

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

gene_metadata_stream_by_post(v1_gene_dataset_request, **kwargs)

Get gene metadata # noqa: E501

Get detailed gene metadata in a streaming, JSON-lines output 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.gene_metadata_stream_by_post(v1_gene_dataset_request, async_req=True)
>>> result = thread.get()
Parameters

v1_gene_dataset_request (V1GeneDatasetRequest) –

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

V1GeneMatch

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

gene_orthologs_by_id(gene_id, **kwargs)

Get gene orthologs by gene ID # noqa: E501

Get detailed gene metadata for an ortholog set by gene ID in a JSON output 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.gene_orthologs_by_id(gene_id, async_req=True)
>>> result = thread.get()
Parameters

gene_id (int) –

Keyword Arguments
  • returned_content (V1OrthologRequestContentType) – Return either gene-ids, or entire gene metadata. [optional]

  • taxon_filter ([str]) – Filter genes by taxa. [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

V1OrthologSet

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

gene_tax_name_query(taxon_query, **kwargs)

Get a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name # noqa: E501

This endpoint retrieves a list of taxonomy names and IDs found in the gene dataset 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.gene_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.

gene_tax_tree(taxon, **kwargs)

Get a taxonomic subtree by taxonomic identifier # noqa: E501

Using an NCBI Taxonomy ID or name (common or scientific) at any rank, get a subtree filtered for species with assembled genomes. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True

>>> thread = api.gene_tax_tree(taxon, async_req=True)
>>> result = thread.get()
Parameters

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

Keyword Arguments
  • children_only (bool) – Only report the children of the requested taxon and not their descendants. [optional] if omitted the server will use the default value of False

  • _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

V1Organism

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

Generated October 22, 2021