gosdk - GenomOncology Software Development Kit

This is a proprietary package that is available from GenomOncology and works with our Knowledge Management System.

For more information about licensing please contact us at:

info@genomoncology.com

Additional proprietary projects available for download via pypi include:

• GO VCF - GenomOncology Variant Call File "call" generator
• GO CLI - GenomOncology Command Line Interface

Our open source projects include:

• Related - Nested Object Models in Python with dictionary, YAML, and JSON transformation support
• Specd - Swagger v2 Specification Directories
• Rigor - HTTP-based DSL for for validating RESTful APIs

Overview

The GenomOncology Software Development Kit (SDK) is to be used with a running instance of the GenomOncology Knowledge Management System. It is built on top of the Specd project and currently provides access to the following functionality:

• Variant HGVS Calculation (g., p., c.)
• Variant Annotation (e.g. gnomAD, dbSNP, etc.)
• Variant Classification (e.g. ACGM or AMP Tiers)
• Gene and Protein Information
• Clinical Trial Matching
• Therapeutic Matching
• Variant Warehouse Loading and Querying

sync mode

When async_enabled is not passed in (default is False) then operation is in "normal" synchronous mode.

TOKEN = "..."
HGVS_G = "NC_000007.13:g.140453136A>T"

from gosdk import construct_sdk
sdk = construct_sdk(token=TOKEN)
a_list = sdk.annotations.get_annotations(batch=[HGVS_G]).result()
annotation = a_list.get_annotation(HGVS_G)
assert annotation.canonical_c_dot == "NM_004333.4:c.1799T>A"

async mode

When async_enabled is True you must then interact with the library using the async/await paradigm.

TOKEN = "..."
HGVS_G = "NC_000007.13:g.140453136A>T"

from gosdk import construct_sdk
sdk = construct_sdk(async_enabled=True, token=TOKEN, loop=loop)
a_list = await sdk.annotations.get_annotations(batch=[HGVS_G]).result()
annotation = a_list.get_annotation(HGVS_G)
assert annotation.canonical_c_dot == "NM_004333.4:c.1799T>A"