Python Library
DNAstack provides a Python client library called dnastack-client-library. This can be used to interact with DNAstack using Python scripts and Jupyter Notebook.
Prerequisite
- Python 3.9 or newer
- Optional:
pip 21.3 or newer- This is only required for ARM-based CPU.
Installation
The library can be installed using pip.
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| pip3 install dnastack-client-library=3.0.56a1648737133
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Setup
Accessing DNAstack services is done by the CollectionServiceClient object.
To initialize, do the following
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| # Import the dnastack-client-library library
from dnastack import CollectionServiceClient
from dnastack.configuration import ServiceEndpoint
# Create the client
api_url = 'https://viral.ai/api/'
client = CollectionServiceClient.make(ServiceEndpoint(adapter_type="collections", url=api_url))
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Usage
List Collections
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| # Import the dnastack-client-library library
from dnastack import CollectionServiceClient
from dnastack.configuration import ServiceEndpoint
# Create the client
api_url = 'https://viral.ai/api/'
client = CollectionServiceClient.make(ServiceEndpoint(adapter_type="collections", url=api_url))
# Get a list of collections
collections = client.list_collections()
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List Collection Tables
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| # Import the dnastack-client-library library
from dnastack import CollectionServiceClient
from dnastack.configuration import ServiceEndpoint
# Create the client
api_url = 'https://viral.ai/api/'
client = CollectionServiceClient.make(ServiceEndpoint(adapter_type="collections", url=api_url))
# Get the Data Connect client for a specific collection
collection_name = 'ncbi-sra'
data_connect_client = client.get_data_connect_client(collection_name)
# Get a list of tables in a collection
tables = data_connect_client.list_tables()
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Query a Collection
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| # Import the dnastack-client-library library
from dnastack import CollectionServiceClient
from dnastack.configuration import ServiceEndpoint
# Create the client
api_url = 'https://viral.ai/api/'
client = CollectionServiceClient.make(ServiceEndpoint(adapter_type="collections", url=api_url))
# Get the Data Connect client for a specific collection
collection_name = 'ncbi-sra'
data_connect_client = client.get_data_connect_client(collection_name)
# Query the collection
query = 'SELECT * FROM collections.ncbi_sra.variants LIMIT 20'
data = data_connect_client.query(query)
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