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gosdk

Project description

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.

```python

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.

```python

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"
```


[GenomOncology]: https://genomoncology.com/
[Knowledge Management System]: https://genomoncology.com/solutions/clinical-oncology/
[Related]: https://github.com/genomoncology/related
[Specd]: https://github.com/genomoncology/specd
[Rigor]: https://github.com/genomoncology/rigor
[GO VCF]: https://pypi.org/project/govcf/
[GO CLI]: https://pypi.org/project/gocli/




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