semvec/pypi-packages huggingface dataset:
ga4gh-client 0.6.0a10
A client for the GA4GH reference server
License: Apache License 2.0
Keywords: genomics,reference

.. image:: http://genomicsandhealth.org/files/logo_ga.png

============
GA4GH Client
============

This is a client library for using the Global Alliance for Genomics and Health (GA4GH) API. This library provides an easy Python programming interface to access GA4GH compliant servers such as the `1kgenomes.ga4gh.org server <http://1kgenomes.ga4gh.org>`_.


**Installation**

::

  pip install ga4gh-client

**To install the latest alpha release use**

::

  pip install --pre ga4gh_client

This installs both the client command line utility and the GA4GH client programming library.

**To demonstrate the CLI try:**

::

  ga4gh_client datasets-search http://1kgenomes.ga4gh.org

**To access the programming API you can use a Python console:**

::

  >>> from ga4gh.client import client
  >>> c = client.HttpClient("http://1kgenomes.ga4gh.org")
  >>> datasets = list(c.search_datasets())
  >>> print datasets
  [id: "WyIxa2dlbm9tZXMiXQ"
  name: "1kgenomes"
  description: "Variants from the 1000 Genomes project and GENCODE genes annotations"
  ]
  >>>

==========
REFERENCES
==========

- For more examples of using the GA4GH client visit this `iPython <https://github.com/BD2KGenomics/bioapi-examples/blob/master/python_notebooks/1kg.ipynb>`_ notebook.
- For more information about GA4GH see the `GA4GH <http://www.genomicsandhealth.org>`_ website.
- Full documentation is available at `read-the-docs.org <http://ga4gh-server.readthedocs.org/en/stable>`_.
- For a quick start with the GA4GH API, please see our `demo <http://ga4gh-server.readthedocs.org/en/stable/demo.html>`_.
- To configure and deploy the GA4GH server in production please see the
  `installation <http://ga4gh-server.readthedocs.org/en/stable/installation.html>`_ page.
- If you would like to contribute to the project, please see the
  `development <http://ga4gh-server.readthedocs.org/en/stable/development.html>`_ page.
ga4gh-schemas 0.6.0a10.post1
GA4GH API Schemas
License: Apache License 2.0
Keywords: genomics,reference

.. image:: http://genomicsandhealth.org/files/logo_ga.png

=============
GA4GH Schemas
=============

This is the GA4GH schemas compiled as `Protocol Buffers <https://developers.google.com/protocol-buffers/>`_
descriptors. It can be used to describe and serialize genomics data using a
standard interchange format.

.. code-block:: python

    import ga4gh.schemas.ga4gh.variants_pb2 as variants
    my_variant = variants.Variant(
        reference_name="1",
        start=1832,
        end=1833,
        reference_bases="A",
        alternate_bases=["C"])

Full documentation is available at `read-the-docs.org
<http://ga4gh-schemas.readthedocs.io/en/stable/>`_.

- To read more about how the GA4GH API uses Protocol Buffers, see `here <http://ga4gh-schemas.readthedocs.io/en/stable/appendix/proto_intro.html>`_.