ncbi-datasets-pylib 16.6.0

Easily gather data from across NCBI databases

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Find and download sequence, annotation and metadata for genes and genomes using this python library with our RESTful API.

This Python library is automatically generated by the OpenAPI Generator project.

Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements

Python >= 3.7

Installation

To install the pre-built python package, create a virtual environment and use pip:

python -m venv ve/
source ve/bin/activate
pip install ncbi-datasets-pylib

Getting Started

Please follow the installation procedure above and then run the following:

import time
import ncbi.datasets.openapi
from pprint import pprint
from ncbi.datasets.openapi.api import gene_api
from ncbi.datasets.openapi.model.rpc_status import RpcStatus
from ncbi.datasets.openapi.model.v1_download_summary import V1DownloadSummary
from ncbi.datasets.openapi.model.v1_fasta import V1Fasta
from ncbi.datasets.openapi.model.v1_gene_dataset_request import V1GeneDatasetRequest
from ncbi.datasets.openapi.model.v1_gene_dataset_request_content_type import V1GeneDatasetRequestContentType
from ncbi.datasets.openapi.model.v1_gene_dataset_request_sort_field import V1GeneDatasetRequestSortField
from ncbi.datasets.openapi.model.v1_gene_match import V1GeneMatch
from ncbi.datasets.openapi.model.v1_gene_metadata import V1GeneMetadata
from ncbi.datasets.openapi.model.v1_organism import V1Organism
from ncbi.datasets.openapi.model.v1_organism_query_request_tax_rank_filter import V1OrganismQueryRequestTaxRankFilter
from ncbi.datasets.openapi.model.v1_ortholog_request_content_type import V1OrthologRequestContentType
from ncbi.datasets.openapi.model.v1_ortholog_set import V1OrthologSet
from ncbi.datasets.openapi.model.v1_sci_name_and_ids import V1SciNameAndIds
from ncbi.datasets.openapi.model.v1_sort_direction import V1SortDirection
# Defining the host is optional and defaults to https://api.ncbi.nlm.nih.gov/datasets/v1
# See configuration.py for a list of all supported configuration parameters.
configuration = ncbi.datasets.openapi.Configuration(
    host = "https://api.ncbi.nlm.nih.gov/datasets/v1"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: ApiKeyAuthHeader
configuration.api_key['ApiKeyAuthHeader'] = 'YOUR_API_KEY'

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['ApiKeyAuthHeader'] = 'Bearer'


# Enter a context with an instance of the API client
with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = gene_api.GeneApi(api_client)
    gene_ids = [
        59067,
    ] # [int] | NCBI gene ids
include_annotation_type = [
        V1Fasta("FASTA_UNSPECIFIED"),
    ] # [V1Fasta] | Select additional types of annotation to include in the data package.  If unset, no annotation is provided. (optional)
fasta_filter = [
        "fasta_filter_example",
    ] # [str] | Limit the FASTA sequences in the datasets package to these transcript and protein accessions (optional)
filename = "ncbi_dataset.zip" # str | Output file name. (optional) (default to "ncbi_dataset.zip")

    try:
        # Get a gene dataset by gene ID
        api_response = api_instance.download_gene_package(gene_ids, include_annotation_type=include_annotation_type, fasta_filter=fasta_filter, filename=filename)
        pprint(api_response)
    except ncbi.datasets.openapi.ApiException as e:
        print("Exception when calling GeneApi->download_gene_package: %s\n" % e)

Documentation for API Endpoints

For detailed documentation of API endpoints, see our GitHub page.

NCBI Datasets command-line tool

Alternatively, you may be interested in trying the NCBI Datasets command-line tools, datasets and dataformat.

Find out more about our command line tools in our documentation.